Enrichment method for variant proteins with altered binding properties

ABSTRACT

A method for selecting novel proteins such as growth hormone and antibody fragment variants having altered binding properties for their respective receptor molecules is provided. The method comprises fusing a gene encoding a protein of interest to the carboxy terminal domain of the gene III coat protein of the filamentous phage M13. The gene fusion is mutated to form a library of structurally related fusion proteins that are expressed in low quantity on the surface of a phagemid particle. Biological selection and screening are employed to identify novel ligands useful as drug candidates. Disclosed are preferred phagemid expression vectors and selected human growth hormone variants.

RELATED APPLICATIONS

This application is a continuation of application Ser. No. 09/717,641filed Nov. 21, 2000; which is a continuation of application Ser. No.08/922,345 filed Sep. 3, 1997; which is a continuation of applicationSer. No. 08/463,587 filed Jun. 5, 1995, now issued as U.S. Pat. No.5,821,047; which is a divisional of application Ser. No. 08/050,058filed Apr. 30, 1993, now issued as U.S. Pat. No. 5,750,373; which is a371 of International Application No. PCT/US91/09133 filed Dec. 3, 1991;which is a continuation-in-part of application Ser. No. 07/743,614 filedAug. 9, 1991, now abandoned; which is a continuation-in-part ofapplication Ser. No. 07/715,300 filed Jun. 14, 1991, now abandoned;which is a continuation-in-part of application Ser. No. 07/683,400 filedApr. 10, 1991, now abandoned; which is a continuation-in-part ofapplication Ser. No. 07/621,667 filed Dec. 3, 1990, now abandoned, thecontents of these applications are incorporated herein by reference.

FIELD OF THE INVENTION

This invention relates to the preparation and systematic selection ofnovel binding proteins having altered binding properties for a targetmolecule. Specifically, this invention relates to methods for producingforeign polypeptides mimicking the binding activity of naturallyoccurring binding partners. In preferred embodiments, the invention isdirected to the preparation of therapeutic or diagnostic compounds thatmimic proteins or nonpeptidyl molecules such a hormones, drugs and othersmall molecules, particularly biologically active molecules such asgrowth hormone.

BACKGROUND OF THE INVENTION

Binding partners are substances that specifically bind to one another,usually through noncovalent interactions. Examples of binding partnersinclude ligand-receptor, antibody-antigen, drug-target, andenzyme-substrate interactions. Binding partners are extremely useful inboth therapeutic and diagnostic fields.

Binding partners have been produced in the past by a variety of methodsincluding; harvesting them from nature (e.g., antibody-antigen, andligand-receptor pairings) and by adventitious identification (e.g.traditional drug development employing random screening of candidatemolecules). In some instances these two approaches have been combined.For example, variants of proteins or polypeptides, such as polypeptidefragments, have been made that contain key functional residues thatparticipate in binding. These polypeptide fragments, in turn, have beenderivatized by methods akin to traditional drug development. An exampleof such derivitization would include strategies such as cyclization toconformationally constrain a polypeptide fragment to produce a novelcandidate binding partner.

The problem with prior art methods is that naturally occurring ligandsmay not have proper characteristics for all therapeutic applications.Additionally, polypeptide ligands may not even be available for sometarget substances. Furthermore, methods for making non-naturallyoccurring synthetic binding partners are often expensive and difficult,usually requiring complex synthetic methods to produce each candidate.The inability to characterize the structure of the resulting candidateso that rational drug design methods can be applied for furtheroptimization of candidate molecules further hampers these methods.

In an attempt to overcome these problems, Geysen (Geysen, Immun. Today,6:364-369 [1985]); and (Geysen et al, Mol. Immun., 23:709-715 [1986])has proposed the use of polypeptide synthesis to provide a framework forsystematic iterative binding partner identification and preparation.According to Geysen et al., Ibid, short polypeptides, such asdipeptides, are first screened for the ability to bind to a targetmolecule. The most active dipeptides are then selected for an additionalround of testing comprising linking, to the starting dipeptide, anadditional residue (or by internally modifying the components of theoriginal starting dipeptide) and then screening this set of candidatesfor the desired activity. This process is reiterated until the bindingpartner having the desired properties is identified.

The Geysen et al. method suffers from the disadvantage that thechemistry upon which it is based, peptide synthesis, produces moleculeswith ill-defined or variable secondary and tertiary structure. As roundsof iterative selection progress, random interactions accelerate amongthe various substituent groups of the polypeptide so that a true randompopulation of interactive molecules having reproducible higher orderstructure becomes less and less attainable. For example, interactionsbetween side chains of amino acids, which are sequentially widelyseparated but which are spatially neighbors, freely occur. Furthermore,sequences that do not facilitate conformationally stable secondarystructures provide complex peptide-sidechain interactions which mayprevent sidechain interactions of a given amino acid with the targetmolecule. Such complex interactions are facilitated by the flexibilityof the polyamide backbone of the polypeptide candidates. Additionally,candidates may exist in numerous conformations making it difficult toidentify the conformer that interacts or binds to the target withgreatest affinity or specificity complicating rational drug design.

A final problem with the iterative polypeptide method of Geysen is that,at present, there are no practical methods with which a great diversityof different peptides can be produced, screened and analyzed. By usingthe twenty naturally occurring amino acids, the total number of allcombinations of hexapeptides that must be synthesized is 64,000,000.Even having prepared such a diversity of peptides, there are no methodsavailable with which mixtures of such a diversity of peptides can berapidly screened to select those peptides having a high affinity for thetarget molecule. At present, each “adherent” peptide must be recoveredin amounts large enough to carry out protein sequencing.

To overcome many of the problems inherent in the Geysen approach,biological selection and screening was chosen as an alternative.Biological selections and screens are powerful tools to probe proteinfunction and to isolate variant proteins with desirable properties(Shortle, Protein Engineering. Oxender and Fox, eds., A. R. Liss, Inc.,NY, pp. 103-108 [1988]) and Bowie et al., Science, 24i:1306-1310[1990)]. However, a given selection or screen is applicable to only oneor a small number of related proteins.

Recently, Smith and coworkers (Smith, Science, 228:1315-1317 [1985]) andParmley and Smith, Gene, 73:305-318 [1985] have demonstrated that smallprotein fragments (10-50 amino acids) can be “displayed” efficiently onthe surface of filamentous phage by inserting short gene fragments intogene III of the fd phage (“fusion phage”). The gene III minor coatprotein (present in about 5 copies at one end of the virion) isimportant for proper phage assembly and for infection by attachment tothe pili of E. coli (see Rasched et al., Microbiol. Rev., 50: 401-427[1986]). Recently, “fusion phage” have been shown to be useful fordisplaying short mutated peptide sequences for identifying peptides thatmay react with antibodies (Scott et al., Science 249: 386-390, [1990])and Cwirla et al., Proc. Natl. Acad. U.S.A 87: 6378-6382, [1990]) or aforeign protein (Devlin et al., Science, 249: 404-406 [1990]).

There are, however, several important limitations in using such “fusionphage” to identify altered peptides or proteins with new or enhancedbinding properties. First, it has been shown (Parmley et al., Gene, 73:305-318, [1988]) that fusion phage are useful only for displayingproteins of less than 100 and preferably less than 50 amino acidresidues, because large inserts presumably disrupt the function of geneIII and therefore phage assembly and infectivity. Second, prior artmethods have been unable to select peptides from a library having thehighest binding affinity for a target molecule. For example, afterexhaustive panning of a random peptide library with an anti-β endorphinmonoclonal antibody, Cwirla and co-workers could not separate moderateaffinity peptides (K_(d)˜10 μM) from higher affinity peptides (K_(d)˜0.4μM) fused to phage. Moreover, the parent β-endorphin peptide sequencewhich has very high affinity (K_(d)˜7 nM), was not panned from theepitope library.

Ladner WO 90/02802 discloses a method for selecting novel bindingproteins displayed on the outer surface of cells and viral particleswhere it is contemplated that the heterologous proteins may have up to164 amino acid residues. The method contemplates isolating andamplifying the displayed proteins to engineer a new family of bindingproteins having desired affinity for a target molecule. Morespecifically, Ladner discloses a “fusion phage” displaying proteinshaving “initial protein binding domains” ranging from 46 residues(crambin) to 164 residues (T4 lysozyme) fused to the M13 gene III coatprotein. Ladner teaches the use of proteins “no larger than necessary”because it is easier to arrange restriction sites in smaller amino acidsequences and prefers the 58 amino acid residue bovine pancreatictrypsin inhibitor (BPTI). Small fusion proteins, such as BPTI, arepreferred when the target is a protein or macromolecule, while largerfusion proteins, such as T4 lysozyme, are preferred for small targetmolecules such as steroids because such large proteins have clefts andgrooves into which small molecules can fit. The preferred protein, BPTI,is proposed to be fused to gene III at the site disclosed by Smith etal. or de la Cruz et al., J. Biol. Chem., 263: 4318-4322 [1988], or toone of the terminii, along with a second synthetic copy of gene III sothat “some” unaltered gene III protein will be present. Ladner does notaddress the problem of successfully panning high affinity peptides fromthe random peptide library which plagues the biological selection andscreening methods of the prior art.

Human growth hormone (hGH) participates in much of the regulation ofnormal human growth and development. This 22,000 dalton pituitaryhormone exhibits a multitude of biological effects including lineargrowth (somatogenesis), lactation, activation of macrophages,insulin-like and diabetogenic effects among others (Chawla, R. K. (1983)Ann. Rev. Med. 34, 519; Edwards, C. K. et al. (1988) Science 239, 769;Thorner, M. O., et al. (1988) J. Clin. Invest. 81, 745). Growth hormonedeficiency in children leads to dwarfism which has been successfullytreated for more than a decade by exogenous administration of hGH. hGHis a member of a family of homologous hormones that include placentallactogens, prolactins, and other genetic and species variants or growthhormone (Nicoll, C. S., et al., (1986) Endocrine Reviews 7, 169). hGH isunusual among these in that it exhibits broad species specificity andbinds to either the cloned somatogenic (Leung, D. W., et al., [1987]Nature 330, 537) or prolactin receptor (Boutin, J. M., et al., [1988]Ce: 53, 69). The cloned gene for hGH has been expressed in a secretedform in Escherichia coli (Chang, C. N., et al., [1987] Gene 55, 189) andits DNA and amino acid sequence has been reported (Goeddel, et al.,[1979] Nature 281, 544; Gray, et al., [1985] Gene 39, 247). Thethree-dimensional structure of hGH is not available. However, thethree-dimensional folding pattern for porcine growth hormone (pGH) hasbeen reported at moderate resolution and refinement (Abdel-Meguid, S.S., et al., [1987] Proc. Natl. Acad. Sci. USA 84, 6434). Human growthhormone's receptor and antibody epitopes have been identified byhomolog-scanning mutagenesis (Cunningham et al., Science 243: 1330,1989). The structure of novel amino terminal methionyl bovine growthhormone containing a spliced-in sequence of human growth hormoneincluding histidine 18 and histidine 21 has been shown (U.S. Pat. No.4,880,910)

Human growth hormone (hGH) causes a variety of physiological andmetabolic effects in various animal models including linear bone growth,lactation, activation of macrophages, insulin-like and diabetogeniceffects and others (R. K. Chawla et al., Annu. Rev. Med. 34, 519 (1983);O. G. P. Isaksson et al., Annu. Rev. Physiol. 47, 483 (1985); C. K.Edwards et al., Science 239, 769 (1988); M. O. Thorner and M. L. Vance,J. Clin. Invest 82, 745 (1988); J. P. Hughes and H. G. Friesen, Ann.Rev. Physiol. 47, 469 (1985)). These biological effects derive from theinteraction between hGH and specific cellular receptors.

Accordingly, it is an object of this invention to provide a rapid andeffective method for the systematic preparation of candidate bindingsubstances.

It is another object of this invention to prepare candidate bindingsubstances displayed on surface of a phagemid particle that areconformationally stable.

It is another object of this invention to prepare candidate bindingsubstances comprising fusion proteins of a phage coat protein and aheterologous polypeptide where the polypeptide is greater than 100 aminoacids in length and may be more than one subunit and is displayed on aphagemid particle where the polypeptide is encoded by the phagemidgenome.

It is a further object of this invention to provide a method for thepreparation and selection of binding substances that is sufficientlyversatile to present, or display, all peptidyl moieties that couldpotentially participate in a noncovalent binding interaction, and topresent these moieties in a fashion that is sterically confined.

Still another object of the invention is the production of growthhormone variants that exhibit stronger affinity for growth hormonereceptor and binding protein.

It is yet another object of this invention to produce expression vectorphagemids that contain a suppressible termination codon functionallylocated between the heterologous polypeptide and the phage coat proteinsuch that detectable fusion protein is produced in a host suppressorcell and only the heterologous polypeptide is produced in anon-suppressor host cell.

Finally, it is an object of this invention to produce a phagemidparticle that rarely displays more than one copy of candidate bindingproteins on the outer surface of the phagemid particle so that efficientselection of high affinity binding proteins can be achieved.

These and other objects of this invention will be apparent fromconsideration of the invention as a whole.

SUMMARY OF THE INVENTION

These objectives have been achieved by providing a method for selectingnovel binding polypeptides comprising: (a) constructing a replicableexpression vector comprising a first gene encoding a polypeptide, asecond gene encoding at least a portion of a natural or wild-type phagecoat protein wherein the first and second genes are heterologous, and atranscription regulatory element operably linked to the first and secondgenes, thereby forming a gene fusion encoding a fusion protein; (b)mutating the vector at one or more selected positions within the firstgene thereby forming a family of related plasmids; (c) transformingsuitable host cells with the plasmids; (d) infecting the transformedhost cells with a helper phage having a gene encoding the phage coatprotein; (e) culturing the transformed infected host cells underconditions suitable for forming recombinant phagemid particlescontaining at least a portion of the plasmid and capable of transformingthe host, the conditions adjusted so that no more than a minor amount ofphagemid particles display more than one copy of the fusion protein onthe surface of the particle; (f) contacting the phagemid particles witha target molecule so that at least a portion of the phagemid particlesbind to the target molecule; and (g) separating the phagemid particlesthat bind from those that do not. Preferably, the method furthercomprises transforming suitable host cells with recombinant phagemidparticles that bind to the target molecule and repeating steps (d)through (g) one or more times.

Additionally, the method for selecting novel binding proteins where theproteins are composed of more than one subunit is achieved by selectingnovel binding peptides comprising constructing a replicable expressionvector comprising a transcription regulatory element operably linked toDNA encoding a protein of interest containing one or more subunits,wherein the DNA encoding at least one of the subunits is fused to theDNA encoding at least a portion of a phage coat protein; mutating theDNA encoding the protein of interest at one or more selected positionsthereby forming a family of related vectors; transforming suitable hostcells with the vectors; infecting the transformed host cells with ahelper phage having a gene encoding the phage coat protein; culturingthe transformed infected host cells under conditions suitable forforming recombinant phagemid particles containing at least a portion ofthe plasmid and capable of transforming the host, the conditionsadjusted so that no more than a minor amount of phagemid particlesdisplay more than one copy of the fusion protein on the surface of theparticle; contacting the phagemid particles with a target molecule sothat at least a portion of the phagemid particles bind to the targetmolecule; and separating the phagemid particles that bind from thosethat do not.

Preferably in the method of this invention the plasmid is under tightcontrol of the transcription regulatory element, and the culturingconditions are adjusted so that the amount or number of phagemidparticles displaying more than one copy of the fusion protein on thesurface of the particle is less than about 1%. Also preferably, amountof phagemid particles displaying more than one copy of the fusionprotein is less than 10% the amount of phagemid particles displaying asingle copy of the fusion protein. Most preferably the amount is lessthan 20%.

Typically, in the method of this invention, the expression vector willfurther contain a secretory signal sequences fused to the DNA encodingeach subunit of the polypeptide, and the transcription regulatoryelement will be a promoter system. Preferred promoter systems areselected from; Lac Z, λ_(PL), TAC, T 7 polymerase, tryptophan, andalkaline phosphatase promoters and combinations thereof.

Also typically, the first gene will encode a mammalian protein,preferably the protein will be selected from; human growth hormone(hGH),N-methionyl human growth hormone, bovine growth hormone, parathyroidhormone, thyroxine, insulin A-chain, insulin B-chain, proinsulin,relaxin A-chain, relaxin B-chain, prorelaxin, glycoprotein hormones suchas follicle stimulating hormone(FSH), thyroid stimulating hormone(TSH),and leutinizing hormone(LH), glycoprotein hormone receptors, calcitonin,glucagon, factor VIII, an antibody, lung surfactant, urokinase,streptokinase, human tissue-type plasminogen activator (t-PA), bombesin,factor IX, thrombin, hemopoietic growth factor, tumor necrosisfactor-alpha and -beta, enkephalinase, human serum albumin,mullerian-inhibiting substance, mouse gonadotropin-associated peptide, amicrobial protein, such as betalactamase, tissue factor protein,inhibin, activin, vascular endothelial growth factor, receptors forhormones or growth factors; integrin, thrombopoietin, protein A or D,rheumatoid factors, nerve growth factors such as NGF-β, platelet-growthfactor, transforming growth factors (TGF) such as TGF-alphaand-TGF-beta, insulin-like growth factor-I and -II, insulin-like growthfactor binding proteins, CD-4, DNase, latency associatedpeptide,-erythropoietin, osteoinductive factors, interferons such asinterferon-alpha, -beta, and -gamma, colony stimulating factors (CSFs)such as M-CSF, GM-CSF, and G-CSF, interleukins (ILs) such as IL-1, IL-2,IL-3, IL-4, superoxide dismutase; decay accelerating factor, viralantigen, HIV envelope proteins such as GP120, GP140, atrial natriureticpeptides A, B or C, immunoglobulins, and fragments of any of theabove-listed proteins.

Preferably the first gene will encode a polypeptide of one or moresubunits containing more than about 100 amino acid residues and will befolded to form a plurality of rigid secondary structures displaying aplurality of amino acids capable of interacting with the target.Preferably the first gene will be mutated at codons corresponding toonly the amino acids capable of interacting with the target so that theintegrity of the rigid secondary structures will be preserved.

Normally, the method of this invention will employ a helper phageselected from; M13KO7, M13R408, M13-VCS, and Phi X 174. The preferredhelper phage is M13KO7, and the preferred coat protein is the M13 Phagegene III coat protein. The preferred host is E. coli, and proteasedeficient strains of E. coli. Novel hGH variants selected by the methodof the present invention have been detected. Phagemid expression vectorswere constructed that contain a suppressible termination codonfunctionally located between the nucleic acids encoding the polypeptideand the phage coat protein.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Strategy for displaying large proteins on the surface offilamentous phage and enriching for altered receptor binding properties.A plasmid, phGH-M13gIII was constructed that fuses the entire codingsequence of hGH to the carboxyl terminal domain of M13 gene III.Transcription of the fusion protein is under control of the lacpromoter/operator sequence, and secretion is directed by the stlI signalsequence. Phagemid particles are produced by infection with the “helper”phage, M13KO7, and particles displaying hGH can be enriched by bindingto an affinity matrix containing the hGH receptor. The wild-type geneIII (derived from the M13KO7 phage) is diagramed by 4-5 copies of themultiple arrows on the tip of the phage, and the fusion protein (derivedfrom the phagemid, phGH-M13gIII) is indicated schematically by thefolding diagram-of hGH replacing the arrow head.

FIG. 2. Immunoblot of whole phage particles shows that hGH comigrateswith phage. Phagemid particles purified in a cesium chloride gradientwere loaded into duplicate wells and electrophoresed through a 1%agarose gel in 375 mM Tris, 40 mM glycine pH 9.6 buffer. The gel wassoaked in transfer buffer (25 mM Tris, pH 8.3, 200 mM glycine, 20%methanol) containing 2% SDS and 2% β-mercaptoethanol for 2 hours, thenrinsed in transfer buffer for 6 hours. The proteins in the gel were thenelectroblotted onto immobilon membranes (Millipore). The membranecontaining one set of samples was stained with Coomassie blue to showthe position of the phage proteins (A). The duplicate membrane wasimmuno-stained for hGH by reacting the membrane with polyclonal rabbitanti-hGH antibodies followed by reaction with horseradish peroxidaseconjugated goat anti-rabbit IgG antibodies (B). Lane 1 contains theM13KO7 parent phage and is visible only in the Coomassie blue stainedmembrane, since it lacks hGH. Lanes 2 and 3 contain separatepreparations of the hormone phagemid particles which is visible both byCoomassie and hGH immuno-staining. The difference in migration distancebetween the parent M13KO7 phage and hormone phagemid particles reflectsthe different size genomes that are packaged within (8.7 kb vs. 5.1 kb,respectively).

FIG. 3. Summary diagram of steps in the selection process for anhGH-phage library randomized at codons 172, 174, 176, and 178. Thetemplate molecules, pH0415, containing a unique KpnI restriction siteand the hGH(R178G,I179T) gene was mutagenized as described in the textand electrotransformed into E. coli strain WJM101 to obtain the initialphagemid library, Library 1. An aliquot (approximately 2%) from Library1 was used directly in an initial selection round as described in thetext to yield Library 1G. Meanwhile, double-stranded DNA (dsDNA) wasprepared from Library 1, digested with restriction enzyme KpnI toeliminate template background, and electrotransformed into WJM101 toyield Library 2. Subsequent rounds of selection (or KpnI digestion,shaded boxes) followed by phagemid propagation were carried out asindicated by the arrows, according to the procedure described in thetext. Four independent clones from Library 4G⁴ and four independentclones from Library 5G⁶ were sequenced by dideoxy sequencing. All ofthese clones had the identical DNA sequence, corresponding to the hGHmutant (Glu 174 Ser, Phe 176 Tyr).

FIG. 4. Structural model of hGH derived from a 2.8 Å folding diagram ofporcine growth hormone determined crystallographicaily. Location ofresidues in hGH that strongly modulate its binding to the hGH-bindingprotein are within the shaded circle. Alanine substitutions that cause agreater than tenfold reduction(o), a four- to tenfold reduction (o), orincrease (O), or a two- to fourfold reduction (o), in binding affinityare indicated. Helical wheel projections in the regions of a-helixreveal their amphipathic quality. Blackened, shaded, or nonshadedresidues are charged, polar, or nonpolar, respectively. In helix-4 themost important residues for mutation are on the hydrophilic face.

FIG. 5. Amino acid substitutions at positions 172, 174, 176 and 178 ofhGH (The notation, e.g. KSYR, denotes hGH mutant 172K/174S/176Y/178R.)found after sequencing a number of clones from rounds 1 and 3 of theselection process for the pathways indicated (hGH elution; Glycineelution; or Glycine elution after pre-adsorption). Non-functionalsequences (i.e. vector background, or other prematurely terminatedand/or frame-shifted mutants) are shown as “NF”. Functional sequenceswhich contained a non-silent, spurious mutation (i.e. outside the set oftarget residues) are marked with a “+“. Protein sequences which appearedmore than once among all the sequenced clones, but with different DNAsequences, are marked with a “#”. Protein sequences which appeared morethan once among the sequenced clones and with the same DNA sequence aremarked with a “*”. Note that after three rounds of selection, 2different contaminating sequences were found; these clones did notcorrespond to cassette mutants, but to previously constructed hormonephage. The pS0643 contaminant corresponds to wild-type hGH-phage (hGH“KEFR” (SEQ ID NO:44)). The pH0457 contaminant, which dominates thethird-round glycine-selected pool of phage, corresponds to a previouslyidentified mutant of hGH, “KSYR.” The amplification of thesecontaminants emphasizes the ability of the hormone-phage selectionprocess to select for rarely occurring mutants. The convergence ofsequences is also striking in all three pathways: R or K occurs mostoften at positions 172 and 178; Y or F occurs most often at position176; and S, T, A, and other residues occur at position 174.

FIG. 6. Sequences from phage selected on hPRLbp-beads in the presence ofzinc. The notation is as described in FIG. 5. Here, the convergence ofsequences is not predictable, but there appears to be a bias towardshydrophobic sequences under the most stringent (Glycine) selectionconditions; L, W and P residues are frequently found in this pool.

FIG. 7. Sequences from phage selected on hPRLbp-beads in the absence ofzinc. The notation is as described in FIG. 5. In contrast to thesequences of FIG. 6, these sequences appear more hydrophilic. After 4rounds of selection using hGH elution, two clones (ANHQ (SEQ ID NO:45),and TLDT/171V (SEQ ID NO:108)) dominate the pool.

FIG. 8. Sequences from phage selected on blank beads. The notation is asdescribed in FIG. 5. After three rounds of selection with glycineelution, no siblings were observed and a background level ofnon-functional sequences remained.

FIG. 9. Construction of phagemid f1 ori from pHO415. This vector forcassette mutagenesis and expression of the hGH-gene III fusion proteinwas constructed as follows. Plasmid pS0643 was constructed byoligonucleotide-directed mutagenesis of pS0132, which contains pBR322and f1 origins of replication and expresses an hGH-gene III fusionprotein (hGH residues 1-191, followed by a single Gly residue, fused toPro-198 of gene III) under the control of the E. coli phoA promoter.Mutagenesis was carried out with the oligonucleotide5′-GGC-AGC-TGT-GGC-TTC-TAG-AGT-GGC-GGC-GGC-TCT-GGT-3′ (SEQ ID NO:1),which introduced a XbaI site (underlined) and an amber stop codon (TAG)following Phe-191 of hGH.

FIG. 10. A. Diagram of plasmid pDH188 insert containing the DNA encodingthe light chain and heavy chain (variable and constant domain 1) of theF_(ab) humanized antibody directed to the HER-2 receptor. V_(L) andV_(H) are the variable regions for the light and heavy chains,respectively. C_(k) is the constant region of the human kappa lightchain. CH1_(G1) is the first constant region of the human gamma 1 chain.Both coding regions start with the bacterial st II signal sequence. B. Aschematic diagram of the entire plasma pDH188 containing the insertdescribed in 5A. After transformation of the plasmid into E. coli SR101cells and the addition of helper phage, the plasmid is packaged intophage particles. Some of these particles display the F_(ab)-P IlI fusion(where p III is the protein encoded by the M13 gene III DNA). Thesegments in the plasmid figure correspond to the insert shown in 5A.

FIG. 11A through C are collectively referred to here as FIG. 11. Thenucleotide (Seq. ID No:24) sequence of the DNA encoding the 4D5 F_(ab)molecule expressed on the phagemid surface. The amino acid sequence ofthe light chain is also shown (Seq. ID No:25 ), as is the amino acidsequence of the heavy chain p III fusion (Seq. ID No:26).

FIG. 12. Enrichment of wild-type 4D5 F_(ab) phagemid from variant F_(ab)phagemid. Mixtures of wild-type phagemid and variant 4D5 Fab phagemid ina ratio of 1:1,000 were selected on plates coated with theextra-cellular domain protein of the HER-2 receptor. After each round ofselection, a portion of the eluted phagemid were infected into E. coliand plasmid DNA was prepared. This plasmid DNA was then digested withEco RV and Pst I, separated on a 5% polyacrylamide gel, and stained withethidium bromide. The bands were visualized under UV light. The bandsdue to the wild-type and variant plasmids are marked with arrows. Thefirst round of selection was eluted only under acid conditions;subsequent rounds were eluted with either an acid elution (left side ofFigure) or with a humanized 4D5 antibody wash step prior to acid elution(right side of Figure) using methods described in Example VIII. Threevariant 4D5 F_(ab) molecules were made: H91A (amino acid histidine atposition 91 on the V_(L) chain mutated to alanine; indicated as ‘A’lanes in Figure), Y49A (amino acid tyrosine at position 49 on the V_(L)chain mutated to alanine; indicated as ‘B’ lanes in the Figure), andY92A (amino acid tyrosine at position 92 on the V_(L) chain mutated toalanine; indicated as ‘C’ lanes in the Figure). Amino acid positionnumbering is according to Kabat et al., (Sequences of proteins ofimmunological interest, 4th ed., U.S. Dept of Health and Human Services,Public Health Service, Nat'l. Institute of Health, Bethesda, Md.[1987]).

FIG. 13. The Scatchard analysis of the RIA affinity determinationdescribed in Experimental Protocols is shown here. The amount of labeledECD antigen that is bound is shown on the x-axis while the amount thatis bound divided by the amount that is free is shown on the y-axis. Theslope of the line indicates the K_(a); the calculated K_(d) is 1/K_(a).

DETAILED DESCRIPTION OF THE INVENTION

The following discussion will be best understood by referring to FIG. 1.In its simplest form, the method of the instant invention comprises amethod for selecting novel binding polypeptides, such as proteinligands, having a desired, usually high, affinity for a target moleculefrom a library of structurally related binding polypeptides. The libraryof structurally related polypeptides, fused to a phage coat protein, isproduced by mutagenesis and, preferably, a single copy of each relatedpolypeptide is displayed on the surface of a phagemid particlecontaining DNA encoding that polypeptide. These phagemid particles arethen contacted with a target molecule and those particles having thehighest affinity for the target are separated from those of loweraffinity. The high affinity binders are then amplified by infection of abacterial host and the competitive binding step is repeated. Thisprocess is reiterated until polypeptides of the desired affinity areobtained.

The novel binding polypeptides or ligands produced by the method of thisinvention are useful per se as diagnostics or therapeutics (eg. agonistsor antagonists) used in treatment of biological organisms. Structuralanalysis of the selected polypeptides may also be used to facilitaterational drug design.

By “binding polypeptide” as used herein is meant any polypeptide thatbinds with a selectable affinity to a target molecule. Preferably thepolypeptide will be a protein that most preferably contains more thanabout 100 amino acid residues. Typically the polypeptide will be ahormone or an antibody or a fragment thereof.

By “high affinity” as used herein is meant an affinity constant (K_(d))of <10⁻⁵ M and preferably <10⁻⁷ M under physiological conditions.

By “target molecule” as used herein is meant any molecule, notnecessarily a protein, for which it is desirable to produce a ligand.Preferably, however, the target will be a protein and most preferablythe target will be a receptor, such as a hormone receptor.

By “humanized antibody” as used herein is meant an antibody in which thecomplementarity-determining regions (CDRs) of a mouse or other non-humanantibody are grafted onto a human antibody framework. By human antibodyframework is meant the entire human antibody excluding the CDRs.

I. Choice of Polypeptides for Display on the Surface of a Phage

The first step in the method of this invention is to choose apolypeptide having rigid secondary structure exposed to the surface ofthe polypeptide for display on the surface of a phage.

By “polypeptide” as used herein is meant any molecule whose expressioncan be directed by a specific DNA sequence. The polypeptides of thisinvention may comprise more than one subunit, where each subunit isencoded by a separate DNA sequence.

By “rigid secondary structure” as used herein is meant any polypeptidesegment exhibiting a regular repeated structure such as is found in;α-helices, 3₁₀ helices, π-helices, parallel and antiparallel β-sheets,and reverse turns. Certain “non-ordered” structures that lackrecognizable geometric order are also included in the definition ofrigid secondary structure provided they form a domain or “patch” ofamino acid residues capable of interaction with a target and that theoverall shape of the structure is not destroyed by replacement of anamino acid within the structure. It is believed that some non-orderedstructures are combinations of reverse turns. The geometry of theserigid secondary structures is well defined by φ and ψ torsional anglesabout the α-carbons of the peptide “backbone”.

The requirement that the secondary structure be exposed to the surfaceof the polypeptide is to provide a domain or “patch” of amino acidresidues that can be exposed to and bind with a target molecule. It isprimarily these amino acid residues that are replaced by mutagenesisthat form the “library” of structurally related (mutant) bindingpolypeptides that are displayed on the surface of the phage and fromwhich novel polypeptide ligands are selected. Mutagenesis or replacementof amino acid residues directed toward the interior of the polypeptideis generally avoided so that the overall structure of the rigidsecondary structure is preserved. Some replacement of amino acids on theinterior region of the rigid secondary structures, especially withhydrophobic amino acid residues, may be tolerated since theseconservative substitutions are unlikely to distort the overall structureof the polypeptide.

Repeated cycles of “polypeptide” selection are used to select for higherand higher affinity binding by the phagemid selection of multiple aminoacid changes which are selected by multiple selection cycles. Followinga first round of phagemid selection, involving a first region orselection of amino acids in the ligand polypeptide, additional rounds ofphagemid selection in other regions or amino acids of the ligandpolypeptide are conducted. The cycles of phagemid selection are repeateduntil the desired affinity properties of the ligand polypeptide areachieved. To illustrate this process, Example VIII phagemid selection ofhGH was conducted in cycles. In the first cycle hGH amino acids 172,174, 176 and 178 were mutated and phagemid selected. In a second cyclehGH amino acids 167, 171, 175 and 179 were phagemid selected. In a thirdcycle hGH amino acids 10, 14, 18 and 21 were phagemid selected. Optimumamino acid changes from a previous cycle may be incorporated into thepolypeptide before the next cycle of selection. For example, hGH aminoacids substitution 174 (serine) and 176 (tyrosine) were incorporatedinto the hGH before the phagemid selection of hGH amino acids 167, 171,175 and 179.

From the forgoing it will be appreciated that the amino acid residuesthat form the binding domain of the polypeptide will not be sequentiallylinked and may reside on different subunits of the polypeptide. That is,the binding domain tracks with the particular secondary structure at thebinding site and not the primary structure. Thus, generally, mutationswill be introduced into codons encoding amino acids within a particularsecondary structure at sites directed away from the interior of thepolypeptide so that they will have the potential to interact with thetarget. By way of illustration, FIG. 2 shows the location of residues inhGH that are known to strongly modulate its binding to the hGH-bindingprotein (Cunningham et al., Science 247:1461-1465 [1990]). Thusrepresentative sites suitable for mutagenesis would include residues172, 174, 176, and 178 on helix-4, as well as residue 64 located in a“non-ordered” secondary structure.

There is no requirement that the polypeptide chosen as a ligand to atarget normally bind to that target. Thus, for example, a glycoproteinhormone such as TSH can be chosen as a ligand for the FSH receptor and alibrary of mutant TSH molecules are employed in the method of thisinvention to produce novel drug candidates.

This invention thus contemplates any polypeptide that binds to a targetmolecule, and includes antibodies. Preferred polypeptides are those thathave pharmaceutical utility. More preferred polypeptides include; agrowth hormone, including human growth hormone, des-N-methionyl humangrowth hormone, and bovine growth hormone; parathyroid hormone; thyroidstimulating hormone; thyroxine; insulin A-chain; insulin B-chain;proinsulin; follicle stimulating hormone; calcitonin; leutinizinghormone; glucagon; factor VIII; an antibody; lung suractant; aplasminogen activator, such as urokinase or human tissue-typeplasminogen activator (t-PA); bombesin; factor IX, thrombin; hemopoieticgrowth factor; tumor necrosis factor-alpha and -beta; enkephalinase; aserum albumin such as human serum albumin; mullerian-inhibitingsubstance; relaxin A-chain; relaxin B-chain; prorelaxin; mousegonadotropin-associated peptide; a microbial protein, such asbetalactamase; tissue factor protein; inhibin; activin; vascularendothelial growth factor; receptors for hormones or growth factors;integrin; thrombopoietin; protein A or D; rheumatoid factors; nervegrowth factor such as NGF-0; platelet-derived growth factor; fibroblastgrowth factor such as aFGF and bFGF; epidermal growth factor;transforming growth factor (TGF) such as TGF-alpha and TGF-beta;insulin-like growth factor-I and -II; insulin-like growth factor bindingproteins; CD-4; DNase; latency associated peptide; erythropoietin;osteoinductive factors; an interferon such as interferon-alpha, -beta,and -gamma; colony stimulating factors (CSFs), e.g., M-CSF, GM-CSF, andG-CSF; interleukins (ILs), e.g., IL-1, IL-2, IL-3, IL-4, etc.;superoxide dismutase; decay accelerating factor; atrial natriureticpeptides A, B or C; viral antigen such as, for example, a portion of theHIV envelope; immunoglobulins; and fragments of any of the above-listedpolypeptides. In addition, one or more predetermined amino acid residueson the polypeptide may be substituted, inserted, or deleted, forexample, to produce products with improved biological properties.Further, fragments of these polypeptides, especially biologically activefragments, are included. Yet more preferred polypeptides of thisinvention are human growth hormone, and atrial naturetic peptides A, B,and C, endotoxin, subtilisin, trypsin and other serine proteases.

Still more preferred are polypeptide hormones that can be defined as anyamino acid sequence produced in a first cell that binds specifically toa receptor on the same cell type (autocrine hormones) or a second celltype (non-autocrine) and causes a physiological response characteristicof the receptor-bearing cell. Among such polypeptide hormones arecytokines, lymphokines, neurotrophic hormones and adenohypophysealpolypeptide hormones such as growth hormone, prolactin, placentallactogen, luteinizing hormone, follicle-stimulating hormone,thyrotropin, chorionic gonadotropin, corticotropin, α orβ-melanocyte-stimulating hormone, β-lipotropin, γ-lipotropin and theendorphins; hypothalmic release-inhibiting hormones such ascorticotropin-release factor, growth hormone release-inhibiting hormone,growth hormone-release factor; and other polypeptide hormones such asatrial natriuretic peptides A, B or C.

II. Obtaining a First Gene (Gene 1) Encoding the Desired Polypeptide

The gene encoding the desired polypeptide (i.e., a polypeptide with arigid secondary structure) can be obtained by methods known in the art(see generally, Sambrook et al. , Molecular Biology: A LaboratoryManual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. [1989]). Ifthe sequence of the gene is known, the DNA encoding the gene may bechemically synthesized (Merrfield, J. Am. Chem. Soc., 85:2149 [1963]).If the sequence of the gene is not known, or if the gene has notpreviously been isolated, it may be cloned from a cDNA library (madefrom RNA obtained from a suitable tissue in which the desired gene isexpressed) or from a suitable genomic DNA library. The gene is thenisolated using an appropriate probe. For cDNA libraries, suitable probesinclude monoclonal or polyclonal antibodies (provided that the cDNAlibrary is an expression library), oligonucleotides, and complementaryor homologous cDNAs or fragments thereof. The probes that may be used toisolate the gene of interest from genomic DNA libraries include cDNAs orfragments thereof that encode the same or a similar gene, homologousgenomic DNAs or DNA fragments, and oligonucleotides. Screening the cDNAor genomic library with the selected probe is conducted using standardprocedures as described in chapters 10-12 of Sambrook et al., supra.

An alternative means to isolating the gene encoding the protein ofinterest is to use polymerase chain reaction methodology (PCR) asdescribed in section 14 of Sambrook et al, supra. This method requiresthe use of oligonucleotides that will hybridize to the gene of interest;thus, at least some of the DNA sequence for this gene must be known inorder to generate the oligonucleotides.

After the gene has been isolated, it may be inserted into a suitablevector (preferably a plasmid) for amplification, as described generallyin Sambrook et al., supra.

III. Constructing Replicable Expression Vectors

While several types of vectors are available and may be used to practicethis invention, plasmid vectors are the preferred vectors for useherein, as they may be constructed with relative ease, and can bereadily amplified. Plasmid vectors generally contain a variety ofcomponents including promoters, signal sequences, phenotypic selectiongenes, origin of replication sites, and other necessary components asare known to those of ordinary skill in the art.

Promoters most commonly used in prokaryotic vectors include the lac Zpromoter system, the alkaline phosphatase pho A promoter, thebacteriophage λPL promoter (a temperature sensitive promoter), the tacpromoter (a hybrid trp-ac promoter that is regulated by the lacrepressor), the tryptophan promoter, and the bacteriophage T7 promoter.For general descriptions of promoters, see section 17 of Sambrook et al.supra. While these are the most commonly used promoters, other suitablemicrobial promoters may be used as well.

Preferred promoters for practicing this invention are those that can betightly regulated such that expression of the fusion gene can becontrolled. It is believed that the problem that went unrecognized inthe prior art was that display of multiple copies of the fusion proteinon the surface of the phagemid particle lead to multipoint attachment ofthe phagemid with the target. It is believed this effect, referred to asthe “chelate effect”, results in selection of false “high affinity”polypeptides when multiple copies of the fusion protein are displayed onthe phagemid particle in close proximity to one another so that thetarget was “chelated”. When multipoint attachment occurs, the effectiveor apparent Kd may be as high as the product of the individual Kds foreach copy of the displayed fusion protein. This effect may be the reasonCwirla and coworkers supra were unable to separate moderate affinitypeptides from higher affinity peptides.

It has been discovered that by tightly regulating expression of thefusion protein so that no more than a minor amount, i.e. fewer thanabout 1%, of the phagemid particles contain multiple copies of thefusion protein the “chelate effect” is overcome allowing properselection of high affinity polypeptides. Thus, depending on thepromoter, culturing conditions of the host are adjusted to maximize thenumber of phagemid particles containing a single copy of the fusionprotein and minimize the number of phagemid particles containingmultiple copies of the fusion protein.

Preferred promoters used to practice this invention are the lac Zpromoter and the pho A promoter. The lac Z promoter is regulated by thelac repressor protein lac i, and thus transcription of the fusion genecan be controlled by manipulation of the level of the lac repressorprotein. By way of illustration, the phagemid containing the lac Zpromotor is grown in a cell strain that contains a copy of the lac irepressor gene, a repressor for the lac Z promotor. Exemplary cellstrains containing the lac i gene include JM 101 and XL1 -blue. In thealternative, the host cell can be cotransfected with a plasmidcontaining both the repressor lac i and the lac Z promotor. Occasionallyboth of the above techniques are used simultaneously, that is, phagmideparticles containing the lac Z promoter are grown in cell strainscontaining the lac i gene and the cell strains are cotransfected with aplasmid containing both the lac Z and lac i genes. Normally when onewishes to express a gene, to the transfected host above one would add aninducer such as isopropylthiogalactoside (IPTG). In the presentinvention however, this step is omitted to (a) minimize the expressionof the gene III fusion protein thereby minimizing the copy number (i.e.the number of gene III fusions per phagemid number) and to (b) preventpoor or improper packaging of the phagemid caused by inducers such asIPTG even at low concentrations. Typically, when no inducer is added,the number of fusion proteins per phagemid particle is about 0.1 (numberof bulk fusion proteins/number of phagemid particles). The mostpreferred promoter used to practice this invention is pho A. Thispromoter is believed to be regulated by the level of inorganic phosphatein the cell where the phosphate acts to down-regulate the activity ofthe promoter. Thus, by depleting cells of phosphate, the activity of thepromoter can be increased. The desired result is achieved by growingcells in a phosphate enriched medium such as 2YT or LB therebycontrolling the expression of the gene III fusion.

One other useful component of vectors used to practice this invention isa signal sequence. This sequence is typically located immediately 5′ tothe gene encoding the fusion protein, and will thus be transcribed atthe amino terminus of the fusion protein. However, in certain cases, thesignal sequence has been demonstrated to be located at positions other5′ to the gene encoding the protein to be secreted. This sequencetargets the protein to which it is attached across the inner membrane ofthe bacterial cell. The DNA encoding the signal sequence may be obtainedas a restriction endonuclease fragment from any gene encoding a proteinthat has a signal sequence. Suitable prokaryotic signal sequences may beobtained from genes encoding, for example, LamB or OmpF (Wong et al.,Gene, 68:193 [1983]), MalE, PhoA and other genes. A preferredprokaryotic signal sequence for practicing this invention is the E. coliheat-stable enterotoxin II (STII) signal sequence as described by Changet al., Gene, 55: 189 [1987].

Another useful component of the vectors used to practice this inventionis phenotypic selection genes. Typical phenotypic selection genes arethose encoding proteins that confer antibiotic resistance upon the hostcell. By way of illustration, the ampicillin resistance gene (amp), andthe tetracycline resistance gene (Let) are readily employed for thispurpose.

Construction of suitable vectors comprising the aforementionedcomponents as well as the gene encoding the desired polypeptide (gene 1)are prepared using standard recombinant DNA procedures as described inSambrook et al. supra. Isolated DNA fragments to be combined to form thevector are cleaved, tailored, and ligated together in a specific orderand orientation to generate the desired vector.

The DNA is cleaved using the appropriate restriction enzyme or enzymesin a suitable buffer. In general, about 0.2-1 μg of plasmid or DNAfragments is used with about 1-2 units of the appropriate restrictionenzyme in about 20 μl of buffer solution. Appropriate buffers, DNAconcentrations, and incubation times and temperatures are specified bythe manufacturers of the restriction enzymes. Generally, incubationtimes of about one or two hours at 37° C. are adequate, although severalenzymes require higher temperatures. After incubation, the enzymes andother contaminants are removed by extraction of the digestion solutionwith a mixture of phenol and chloroform, and the DNA is recovered fromthe aqueous fraction by precipitation with ethanol.

To ligate the DNA fragments together to form a functional vector, theends of the DNA fragments must be compatible with each other. In somecases, the ends will be directly compatible after endonucleasedigestion. However, it may be necessary to first convert the sticky endscommonly produced by endonuclease digestion to blunt ends to make themcompatible for ligation. To blunt the ends, the DNA is treated in asuitable buffer for at least 15 minutes at 15° C. with 10 units of theKlenow fragment of DNA polymerase I (Klenow) in the presence of the fourdeoxynucleotide triphosphates. The DNA is then purified byphenol-chloroform extraction and ethanol precipitation.

The cleaved DNA fragments may be size-separated and selected using DNAgel electrophoresis. The DNA may be electrophoresed through either anagarose or a polyacrylamide matrix. The selection of the matrix willdepend on the size of the DNA fragments to be separated. Afterelectrophoresis, the DNA is extracted from the matrix by electroelution,or, if low-melting agarose has been used as the matrix, by melting theagarose and extracting the DNA from it, as described in sections6.30-6.33 of Sambrook et al., supra.

The DNA fragments that are to be ligated together (previously digestedwith the appropriate restriction enzymes such that the ends of eachfragment to be ligated are compatible) are put in solution in aboutequimolar amounts. The solution will also contain ATP, ligase buffer anda ligase such as T4 DNA ligase at about 10 units per 0.5 μg of DNA. Ifthe DNA fragment is to be ligated into a vector, the vector is at firstlinearized by cutting with the appropriate restriction endonuclease(s).The linearized vector is then treated with alkaline phosphatase or calfintestinal phosphatase. The phosphatasing prevents self-ligation of thevector during the ligation step.

After ligation, the vector with the foreign gene now inserted istransformed into a suitable host cell. Prokaryotes are the preferredhost cells for this invention. Suitable prokaryotic host cells includeE. coli strain JM101, E. coli K12 strain 294 (ATCC number 31,446), E.coli strain W3110 (ATCC number 27,325), E. coli X1776 (ATCC number31,537), E. coli XL-1 Blue (stratagene), and E. coli B; however manyother strains of E. coli, such as HB101, NM522, NM538, NM539, and manyother species and genera of prokaryotes may be used as well. In additionto the E. coli strains listed above, bacilli such as Bacillus subtilis,other enterobacteriaceae such as Salmonella typhimurium or Serratiamarcesans, and various Pseudomonas species may all be used as hosts.

Transformation of prokaryotic cells is readily accomplished using thecalcium chloride method as described in section 1.82 of Sambrook et al.,supra. Alternatively, electroporation (Neumann et al., EMBO J., 1:841[1982]) may be used to transform these cells. The transformed cells areselected by growth on an antibiotic, commonly tetracycline (tet) orampicillin (amp), to which they are rendered resistant due to thepresence of tet and/or amp resistance genes on the vector.

After selection of the transformed cells, these cells are grown inculture and the plasmid DNA (or other vector with the foreign geneinserted) is then isolated. Plasmid DNA can be isolated using methodsknown in the art. Two suitable methods are the small scale preparationof DNA and the large-scale preparation of DNA as described in sections1.25-1.33 of Sambrook et al., supra. The-isolated DNA can be purified bymethods known in the art such as that described in section 1.40 ofSambrook et al., supra. This purified plasmid DNA is then analyzed byrestriction mapping and/or DNA sequencing. DNA sequencing is generallyperformed by either the method of Messing et al. Nucleic Acids Res,9:309 [1981] or by the method of Maxam et al. Meth. Enzymol., 65: 499[1980].

IV. Gene Fusion

This invention contemplates fusing the gene enclosing the desiredpolypeptide (gene 1) to a second gene (gene 2) such that a fusionprotein is generated during transcription. Gene 2 is typically a coatprotein gene of a phage, and preferably it is the phage M13 gene IIIcoat protein, or a fragment thereof. Fusion of genes 1 and 2 may beaccomplished by inserting gene 2 into a particular site on a plasmidthat contains gene 1, or by inserting gene 1 into a particular site on aplasmid that contains gene 2.

Insertion of a gene into a plasmid requires that the plasmid be cut atthe precise location that the gene is to be inserted. Thus, there mustbe a restriction endonuclease site at this location (preferably a uniquesite such that the plasmid will only be cut at a single location duringrestriction endonuclease digestion). The plasmid is digested,phosphatased, and purified as described above. The gene is then insertedinto this linearized plasmid by ligating the two DNAs together. Ligationcan be accomplished if the ends of the plasmid are compatible with theends of the gene to be inserted. If the restriction enzymes are used tocut the plasmid and isolate the gene to be inserted create blunt ends orcompatible sticky ends, the DNAs can be ligated together directly usinga ligase such as bacteriophage T4 DNA ligase and incubating the mixtureat 16° C. for 1-4 hours in the presence of ATP and ligase buffer asdescribed in section 1.68 of Sambrook et al., supra. If the ends are notcompatible, they must first be made blunt by using the Klenow fragmentof DNA polymerase I or bacteriophage T4 DNA polymerase, both of whichrequire the four deoxyribonucleotide triphosphates to fill-inoverhanging single-stranded ends of the digested DNA. Alternatively, theends may be blunted using a nuclease such as nuclease S1 or mung-beannuclease, both of which function by cutting back the overhanging singlestrands of DNA. The DNA is then religated using a ligase as describedabove. In some cases, it may not be possible to blunt the ends of thegene to be inserted, as the reading frame of the coding region will bealtered. To overcome this problem, oligonucleotide linkers may be used.The linkers serve as a bridge to connect the plasmid to the gene to beinserted. These linkers can be made synthetically as double stranded orsingle stranded DNA using standard methods. The linkers have one endthat is compatible with the ends of the gene to be inserted; the linkersare first ligated to this gene using ligation methods described above.The other end of the linkers is designed to be compatible with theplasmid for ligation. In designing the linkers, care must be taken tonot destroy the reading frame of the gene to be inserted or the readingframe of the gene contained on the plasmid. In some cases, it may benecessary to design the linkers such that they code for part of an aminoacid, or such that they code for one or more amino acids.

Between gene 1 and gene 2, DNA encoding a termination codon may beinserted, such termination codons are UAG (amber), UM (ocher) and UGA(opel). (Microbiology, Davis et al. Harper & Row, New York, 1980, pages237, 245-47 and 274). The termination codon expressed in a wild typehost cell results in the synthesis of the gene 1 protein product withoutthe gene 2 protein attached. However, growth in a suppressor host cellresults in the synthesis of detectable quantities of fused protein. Suchsuppressor host cells contain a tRNA modified to insert an amino acid inthe termination codon position of the mRNA thereby resulting inproduction of detectible amounts of the fusion protein. Such suppressorhost cells are well known and described, such as E. coli suppressorstrain (Bullock et al., BioTechniques 5, 376-379 [1987]). Any acceptablemethod may be used to place such a termination codon into the mRNAencoding the fusion polypeptide.

The suppressible codon may be inserted between the first gene encoding apolypeptide, and a second gene encoding at least a portion of a phagecoat protein. Alternatively, the suppressible termination codon may beinserted adjacent to the fusion site by replacing the last amino acidtriplet in the polypeptide or the first amino acid in the phage coatprotein. When the phagemid containing the suppressible codon is grown ina suppressor host cell, it results in the detectable production of afusion polypeptide containing the polypeptide and the coat protein. Whenthe phagemid is grown in a non-suppressor host cell, the polypeptide issynthesized substantially without fusion to the phage coat protein dueto termination at the inserted suppressible triplet encoding UAG, UAA,or UGA. In the non-suppressor cell the polypeptide is synthesized andsecreted from the host cell due to the absence of the fused phage coatprotein which otherwise anchored it to the host cell.

V. Alteration(mutation) of Gene 1 at Selected Positions

Gene 1, encoding the desired polypeptide, may be altered at one or moreselected codons. An alteration is defined as a substitution, deletion,or insertion of one or more codons in the gene encoding the polypeptidethat results in a change in the amino acid sequence of the polypeptideas compared with the unaltered or native sequence of the samepolypeptide. Preferably, the alterations will be by substitution of atleast one amino acid with any other amino acid in one or more regions ofthe molecule. The alterations may be produced be a variety of methodsknown in the art. These methods include but are not limited tooligonucleotide-mediated mutagenesis and cassette mutagenesis.

A. Oligonucleotide-Mediated Mutagenesis

Oligonucleotide-mediated mutagenesis is preferred method for preparingsubstitution, deletion, and insertion variants of gene 1. This techniqueis well known in the art as described by Zoller et al. Nucleic AcidsRes. 10: 6487-6504 [1987]. Briefly, gene 1 is altered by hybridizing anoligonucleotide encoding the desired mutation to a DNA template, wherethe template is the single-stranded form of the plasmid containing theunaltered or native DNA sequence of gene 1. After hybridization, a DNApolymerase is used to synthesize an entire second complementary strandof the template will thus incorporate the oligonucleotide primer, andwill code for the selected alteration in gene 1.

Generally, oligonucleotides of at least 25 nucleotides in length areused. An optimal oligonucleotide will have 12 to 15 nucleotides that arecompletely complementary to the template on either side of thenucleotide(s) coding for the mutation. This ensures that theoligonucleotide will hybridize properly to the single-stranded DNAtemplate molecule. The oligonucleotides are readily synthesized usingtechniques known in the art such as that described by Crea et al. Proc.Nat'l. Acad. Sci. USA, 75: 5765 [1978]:

The DNA template can only be generated by those vectors that are eitherderived from bacteriophage M13 vectors (the commercially availableM13mp18 and M13mp19 vectors are suitable), or those vectors that containa single-stranded phage origin of replication as described by Viera etal. Meth. Enzymol., 153: 3 [1987]. Thus, the DNA that is to be mutatedmust be inserted into one of these vectors in order to generatesingle-stranded template. Production of the single-stranded template isdescribed in sections 4.21-4.41 of Sambrook et al., supra.

To alter the native DNA sequence, the oligonucleotide is hybridized tothe single stranded template under suitable hybridization conditions. ADNA polymerizing enzyme, usually the Klenow fragment of DNA polymeraseI, is then added to synthesize the complementary strand of the templateusing the oligonucleotide as a primer for synthesis. A heteroduplexmolecule is thus formed such that one strand of DNA encodes the mutatedform of gene 1, and the other strand (the original template) encodes thenative, unaltered sequence of gene 1. This heteroduplex molecule is thentransformed into a suitable host cell, usually a prokaryote such as E.Coli JM101. After growing the cells, they are plated onto agarose platesand screened using the oligonucleotide primer radiolabelled with32-Phosphate to identify the bacterial colonies that contain the mutatedDNA.

The method described immediately above may be modified such that ahomoduplex molecule is created wherein both strands of the plasmidcontain the mutation(s). The modifications are as follows: Thesingle-stranded oligonucleotide is annealed to the single-strandedtemplate as described above. A mixture of three deoxyribonucleotides,deoxyriboadenosine (dATP), deoxyriboguanosine (dGTP), anddeoxyribothymidine (dTTP), is combined with a modifiedthio-deoxyribocytosine called dCTP-(aS) (which can be obtained fromAmersham). This mixture is added to the template-oligonucleotidecomplex. Upon addition of DNA polymerase to this mixture, a strand ofDNA identical to the template except for the mutated bases is generated.In addition, this new strand of DNA will contain dCTP-(aS) instead ofdCTP, which serves to protect it from restriction endonucleasedigestion. After the template strand of the double-stranded heteroduplexis nicked with an appropriate restriction enzyme, the template strandcan be digested with ExoIII nuclease or another appropriate nucleasepast the region that contains the site(s) to be mutagenized. Thereaction is then stopped to leave a molecule that is only partiallysingle-stranded. A complete double-stranded DNA homoduplex is thenformed using DNA polymerase in the presence of all fourdeoxyribonucleotide triphosphates, ATP, and DNA ligase. This homoduplexmolecule can then be transformed into a suitable host cell such as E.coli JM101, as described above.

Mutants with more than one amino acid to be substituted may be generatedin one of several ways. If the amino acids are located close together inthe polypeptide chain, they may be mutated simultaneously using oneoligonucleotide that codes for all of the desired amino acidsubstitutions. If, however, the amino acids are located some distancefrom each other (separated by more than about ten amino acids), it ismore difficult to generate a single oligonucleotide that encodes all ofthe desired changes. Instead, one of two alternative methods may beemployed.

In the first method, a separate oligonucleotide is generated for eachamino acid to be substituted. The oligonucleotides are then annealed tothe single-stranded template DNA simultaneously, and the second strandof DNA that is synthesized from the template will encode all of thedesired amino acid substitutions. The alternative method involves two ormore rounds of mutagenesis to produce the desired mutant. The firstround is as described for the single mutants: wild-type DNA is used forthe template, an oligonucleotide encoding the first desired amino acidsubstitution(s) is annealed to this template, and the heteroduplex DNAmolecule is then generated. The second round of mutagenesis utilizes themutated DNA produced in the first round of mutagenesis as the template.Thus, this template already contains one or more mutations. Theoligonucleotide encoding the additional desired amino acidsubstitution(s) is then annealed to this template, and the resultingstrand of DNA now encodes mutations from both the first and secondrounds of mutagenesis. This resultant DNA can be used as a template in athird round of mutagenesis, and so-on.

B. Cassette Mutagenesis

This method is also a preferred method for preparing substitution,deletion, and insertion variants of gene 1. The method is based on thatdescribed by Wells et al. Gene, 34:315 [1985]. The starting material isthe plasmid (or other vector) comprising gene 1, the gene to be mutated.The codon(s) in gene 1 to be mutated are identified. There must be aunique restriction endonuclease site on each side of the identifiedmutation site(s). If no such restriction sites exist, they may begenerated using the above-described oligonucleotide-mediated mutagenesismethod to introduce them at appropriate locations in gene 1. After therestriction sites have been introduced into the plasmid, the plasmid iscut at these sites to linearize it. A double-stranded oligonucleotideencoding the sequence of the DNA between the restriction sites butcontaining the desired mutation(s) is synthesized using standardprocedures. The two strands are synthesized separately and thenhybridized together using standard techniques. This double-strandedoligonucleotide is referred to as the cassette. This cassette isdesigned to have 3′ and 5′ ends that are compatible with the ends of thelinearized plasmid, such that it can be directly ligated to the plasmid.This plasmid now contains the mutated DNA sequence of gene 1.

VI. Obtaining DNA Encoding the Desired Protein

In an alternative embodiment, this invention contemplates production ofvariants of a desired protein containing one or more subunits. Eachsubunit is typically encoded by separate gene. Each gene encoding eachsubunit can be obtained by methods known in the art (see, for example,Section II). In some instances, it may be necessary to obtain the geneencoding the various subunits using separate techniques selected fromany of the methods described in Section II.

When constructing a replicable expression vector where the protein ofinterest contains more than one subunit, all subunits can be regulatedby the same promoter, typically located 5′ to the DNA encoding thesubunits, or each may be regulated by separate promoter suitablyoriented in the vector so that each promoter is operably linked to theDNA it is intended to regulate. Selection of promoters is carried out asdescribed in Section III above.

In constructing a replicable expression vector containing DNA encodingthe protein of interest having multiple subunits, the reader is referredto FIG. 10 where, by way of illustration, a vector is diagrammed showingDNA encoding each subunit of an antibody fragment. This figure showsthat, generally, one of the subunits of the protein of interest will befused to a phage coat protein such as M13 gene III. This gene fusiongenerally will contain its own signal sequence. A separate gene encodesthe other subunit or subunits, and it is apparent that each subunitgenerally has its own signal sequence. FIG. 10 also shows that a singlepromoter can regulate the expression of both subunits. Alternatively,each subunit may be independently regulated by a different promoter. Theprotein of interest subunit-phage coat protein fusion construct can bemade as described in Section IV above.

When constructing a family of variants of the desired multi-subunitprotein, DNA encoding each subunit in the vector may mutated in one ormore positions in each subunit. When multi-subunit antibody variants areconstructed, preferred sites of mutagenesis correspond to codonsencoding amino acid residues located in the complementarity-determiningregions (CDR) of either the light chain, the heavy chain, or bothchains. The CDRs are commonly referred to as the hypervariable regions.Methods for mutagenizing DNA encoding each subunit of the protein ofinterest are conducted essentially as described in Section V above.

VII. Preparing a Target Molecule and Binding with Phagemid

Target proteins, such as receptors, may be isolated from natural sourcesor prepared by recombinant methods by procedures known in the art. Byway of illustration, glycoprotein hormone receptors may be prepared bythe technique described by McFarland et al., Science 245:494-499 [1989],nonglycosylated forms expressed in E. coli are described by Fuh et al.J. Biol. Chem 265:3111-3115 [1990] Other receptors can be prepared bystandard methods.

The purified target protein may be attached to a suitable matrix such asagarose beads, acrylamide beads, glass beads, cellulose, various acryliccopolymers, hydroxylalkyl methacrylate gels, polyacrylic andpolymethacrylic copolymers, nylon, neutral and ionic carriers, and thelike. Attachment of the target protein to the matrix may be accomplishedby methods described in Methods in Enzymology. 44 [1976], or by othermeans known in the art.

After attachment of the target protein to the matrix, the immobilizedtarget is contacted with the library of phagemid particles underconditions suitable for binding of at least a portion of the phagemidparticles with the immobilized target. Normally, the conditions,including pH, ionic strength, temperature and the like will-mimicphysiological conditions.

Bound phagemid particles (“binders”) having high affinity for theimmobilized target are separated from those having a low affinity (andthus do not bind to the target) by washing. Binders may be dissociatedfrom the immobilized target by a variety of methods. These methodsinclude competitive dissociation using the wild-type ligand, altering pHand/or ionic strength, and methods known in the art.

Suitable host cells are infected with the binders and helper phage, andthe host cells are cultured under conditions suitable for amplificationof the phagemid particles. The phagemid particles are then collected andthe selection process is repeated one or more times until binders havingthe desired affinity for the target molecule are selected.

Optionally the library of phagemid particles may be sequentiallycontacted with more than one immobilized target to improve selectivityfor a particular target. For example, it is often the case that a ligandsuch as hGH has more than one natural receptor. In the case of hGH, boththe growth hormone receptor and the prolactin receptor bind the hGHligand. It may be desirable to improve the selectivity of hGH for thegrowth hormone receptor over the prolactin receptor. This can beachieved by first contacting the library of phagemid particles withimmobilized prolactin receptor, eluting those with a low affinity (i.e.lower than wild type hGH) for the prolactin receptor and then contactingthe low affinity prolactin “binders” or non-binders with the immobilizedgrowth hormone receptor, and selecting for high affinity growth hormonereceptor binders. In this case an hGH mutant having a lower affinity forthe prolactin receptor would have therapeutic utility even if theaffinity for the growth hormone receptor were somewhat lower than thatof wild type hGH. This same strategy may be employed to improveselectivity of a particular hormone or protein for its primary functionreceptor over its clearance receptor.

In another embodiment of this invention, an improved substrate aminoacid sequence can be obtained. These may be useful for making better“cut sites” for protein linkers, or for better proteasesubstrates/inhibitors. In this embodiment, an immobilizable molecule(e.g. hGH-receptor, biotin-avidin, or one capable of covalent linkagewith a matrix) is fused to gene III through a linker. The linker willpreferably be from 3 to 10 amino acids in length and will act as asubstrate for a protease. A phagemid will be constructed as describedabove where the DNA encoding the linker region is randomly mutated toproduce a randomized library of phagemid particles with different aminoacid sequences at the linking site. The library of phagemid particlesare then immobilized on a matrix and exposed to a desired protease.Phagemid particles having preferred or better substrate amino acidsequences in the liner region for the desired protease will be eluted,first producing an enriched pool of phagemid particles encodingpreferred linkers. These phagemid particles are then cycled several moretimes to produce an enriched pool of particles encoding consensesequence(s) (see examples XIII and XIV).

VIII. Growth Hormone Variants and Methods of Use

The cloned gene for hGH has been expressed in a secreted form inEschericha coli (Chang, C. N>, et al., [1987] Gene 55 189) and its DNAand-amino acid sequence has been reported (Goeddel, et al. [1979] Nature281 544; Gray et al., [1985] Gene 39, 247). The present inventiondescribes novel hGH variants produced using the phagemid selectionmethods. Human growth hormone variants containing substitutions atpositions 10, 14, 18, 21, 167, 171, 172, 174, 175, 176, 178 and 179 havebeen described. Those having higher binding affinities are described inTables VII, XIII and XIV. The amino acid nomenclature for describing thevariants is shown below. Growth hormone variants may be administered andformulated in the same manner as regular growth hormone. The growthhormone variants of the present invention may be expressed in anyrecombinant system which is capable of expressing native or met hGH.

Therapeutic formulations of hGH for therapeutic administration areprepared for storage by mixing hGH having the desired degree of puritywith optional physiologically acceptable carriers, excipients, orstabilizers (Remington's Pharmaceutical Sciences, 16th edition, Osol,A., Ed., (1980)., in the form of lyophilized cake or aqueous solutions.Acceptable carriers, excipients or stabilizers are nontoxic torecipients at the dosages and concentrations employed, and includebuffers such as phosphate, citrate, and other organic acids;antioxidants including ascorbic acid; low molecular weight (less thanabout 10 residues) polypeptides; proteins, such as serum albumin,gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids such as glycine, glutamine,asparagine, arginine, or lysine; monosaccharides, disaccharides, andother carbohydrates including glucose, mannose, or dextrins; chelatingagents such as EDTA; divalent metal ions such as zinc, cobalt or copper;sugar alcohols such as mannitol or sorbitol; salt-forming counterionssuch as sodium; and/or nonionic surfactants such as Tween, Pluronics orpolyethylene glycol (PEG). Formulations of the present invention mayadditionally contain a pharmaceutically acceptable buffer, amino acid,bulking agent and/or non-ionic surfactant. These include, for example,buffers, chelating agents, antioxidants, preservatives, cosolvents, andthe like; specific examples of these could include, trimethylamainesalts (“Tris buffer”), and disodium edetate. The phagemids of thepresent invention may be used to produce quantities of the hGH variantsfree of the phage protein. To express hGH variants free of the gene IIIportion of the fusion, pS0643 and derivatives can simply be grown in anon-suppressor strain such as 16C9. In this case, the amber codon (TAG)leads to termination of translation, which yields free hormone, withoutthe need for an independent DNA construction. The hGH variant issecreted from the host and may be isolated from the culture medium.

One or more of the eight hGH amino acids F10, M14, H18, H21, R167, D171,T175 and I179 may be replaced by any amino acid other than the one foundin that position in naturally occurring hGH as indicated. Therefore, 1,2, 3, 4, 5, 6, 7, or all 8 of the indicated amino acids, F10, M14, H18,H21, R167, D171, T175 and I179, may be replaced by any of the other 19amino acids out of the 20 amino acids listed below. In a preferredembodiment, all eight listed amino acids are replaced by another aminoacid. The most preferred eight amino acids to be substituted areindicated in Table XIV in Example XII. Amino acid nomenclature. Ala (A)Arg (R) Asn (N) Asp (D) Cys (C) Gln (Q) Glu (E) Gly (G) His (H) Ile (I)Leu (L) Lys (K) Met (M) Phe (F) Pro (P) Ser (S) Thr (T) Trp (W) Tyr (Y)Val (V)The one letter hGH variant nomenclature first gives the hGH amino aciddeleted, for example glutamate 179; then the amino acid inserted; forexample, serine; resulting in (E1795S).

EXAMPLES

Without further description, it is believed that one of ordinary skillin the art can, using the preceding description and illustrativeexamples, make and utilize the present invention to the fullest extent.The following working examples therefore specifically point outpreferred embodiments of the present invention, and are not to beconstrued as limiting in any way of the remainder of the disclosure.

Example I Plasmid Constructions and Preparation of hGH-PhagemidParticles

The plasmid phGH-M13gIII (FIG. 1), was constructed from M13KO7⁷ and thehGH producing plasmid, pBO473 (Cunningham, B. C., et al., Science,243:1330-1336, [1989]). A synthetic oligonucleotide5′-AGC-TGT-GGC-TTC-GGG-CCC-TTA-GCA-TTT-AAT-GCG-GTA-3′ (SEQ ID NO:2) wasused to introduce a unique ApaI restriction site (underlined) intopBO473 after the final Phe191 codon of hGH. The oligonucleotide5′-TTC-ACA-AAC-GAA-GGG-CCC-CTA-ATT-AAA-GCC-AGA-3′ (SEQ ID NO:3) was usedto introduce a unique ApaI restriction site (underlined), and aGlu197-to-amber stop codon (bold lettering) into M13KO7 gene III. Theoligonucleotide 5′-CAA-TAA-TAA-CGG-GCT-AGC-CAA-AAG-AAC-TGG-3′ (SEQ IDNO:4) introduces a unique NheI site (underlined) after the 3′ end of thegene III coding sequence. The resulting 650 base pair (bp) ApaI-NheIfragment from the doubly mutated M13KO7 gene III was cloned into thelarge ApaI-NheI fragment of pBO473 to create the plasmid, pSO132. Thisfuses the carboxyl terminus of hGH (Phe191) to the Pro198 residue of thegene III protein with the insertion of a glycine residue encoded fromthe ApaI site and places the fusion protein under control of the E. colialkaline phosphatase (phoA) promoter and stlI secretion signal sequence(Chang, C. N., et al. , Gene, 55:189-196, [1987]). For inducibleexpression of the fusion protein in rich media, we replaced the phoApromoter with the lac promoter and operator. A 138 bp EcoRI-XbaIfragment containing the lac promoter, operator, and Cap binding site wasproduced by PCR of plasmid pUC119 using the oligonucleotides5′-CACGACAGAATTCCCGACTGGAAA-3′ (SEQ ID NO:5) and 5′-CTGTTTCTAGAGTGAAATTGTTA-3′ (SEQ ID NO:6) that flank the desired lac sequencesand introduce the EcoRI and XbaI restriction sites (underlined). Thislac fragment was gel purified and ligated into the large EcoRI-XbaIfragment of pSO132 to create the plasmid, phGH-M13gIII. The sequences ofall tailored DNA junctions were verified by the dideoxy sequence method(Sanger, F., et al. Proc. Natl. Acad. Sci. U.S.A. 74:5463-5467, [1977]).The R64A variant hGH phagemid was constructed as follows: the NsiI-BgIIImutated fragment of hGH (Cunningham et al. supra) encoding the Arg64 toAla substitution (R64A) (Cunningham, B. C., Wells, J. A., Science,244:1081-1085, [1989]) was cloned between the corresponding restrictionsites in the phGH-M13gIII plasmid (FIG. 1) to replace the wild-type hGHsequence. The R64A hGH phagemid particles were propagated and titered asdescribed below for the wild-type hGH-phagemid.

Plasmids were transformed into a male strain of E. coli (JM101) andselected on carbenicillin plates. A single transformant was grown in 2ml 2YT medium for 4 h at 37° C. and infected with 50 μl of M13KO7 helperphage. The infected culture was diluted into 30 ml 2YT, grown overnight,and phagemid particles were harvested by precipitation with polyethyleneglycol (Vierra, J., Messing, J., Methods in Enzymology, 153:3-11,[1987]). Typical phagemid particle titers ranged from 2 to 5×10¹¹cfu/ml. The particles were purified to homogeneity by CsCl densitycentrifugation (Day, L. A. J. Mol. Biol., 39:265-277, [1969]) to removeany fusion protein not attached to virions.

Example II Immunochemical Analyses of hGH on the Fusion Phage

Rabbit polyclonal antibodies to hGH were purified with protein A, andcoated onto microtiter plates (Nunc) at a concentration of 2 μg/ml in 50mM sodium carbonate buffer (pH 10) at 4° C. for 16-20 hours. Afterwashing in PBS containing 0.05% Tween 20, hGH or hGH-phagemid particleswere serially diluted from 2.0-0.002 nM in buffer A (50 mM Tris (pH7.5), 50 mM NaCl, 2 mM EDTA, 5 mg/ml bovine serum albumin, and 0.05%Tween 20). After 2 hours at room temperature (rt), the plates werewashed well and the indicated Mab (Cunningham et al. supra) was added at1 μg/ml in buffer A for 2 hours at rt. Following washing, horseradishperoxidase conjugated goat anti-mouse IgG antibody was bound at rt for 1hour. After a final wash, the peroxidase activity was assayed with thesubstrate, o-phenylenediamine.

Example III Coupling of the hGH Binding Protein to Polyacrylamide Beadsand Binding Enrichments

Oxirane polyacrylamide beads (Sigma) were conjugated to the purifiedextracellular domain of the hGH receptor (hGHbp) (Fuh, G., et al., J.Biol. Chem., 265:3111-3115 [1990]) containing an extra cysteine residueintroduced by site-directed mutagenesis at position 237 that does notaffect binding of hGH (J. Wells, unpublished). The hGHbp was conjugatedas recommended by the supplier to a level of 1.7 pmol hGHbp/mg dryoxirane bead, as measured by binding of [¹²⁵I] hGH to the resin.Subsequently, any unreacted oxirane groups were blocked with BSA andTris. As a control for non-specific binding of phagemid particles, BSAwas similarly coupled to the beads. Buffer for adsorption and washingcontained 10 mM Tris.HCl (pH 7.5), 1 mM EDTA, 50 mM NaCl, 1 mg/ml BSA,and 0.02% Tween 20. Elution buffers contained wash buffer plus 200 nMhGH or 0.2 M glycine (pH 2.1). Parental phage M13KO7 was mixed with hGHphagemid particles at a ratio of nearly 3000:1 (original mixture) andtumbled for 8-12 h with a 5 μl aliquot (0.2 mg of acrylamide beads) ofeither absorbent in a 50 μl volume at room temperature. The beads werepelleted by centrifugation and the supernate carefully removed. Thebeads were resuspended in 200 μl wash buffer and tumbled at roomtemperature for 4 hours (wash 1). After a second wash (wash 2), thebeads were eluted twice with 200 nM hGH for 6-10 hours each (eluate 1,eluate 2). The final elution was with a glycine buffer (pH 2.1) for 4hours to remove remaining hGH phagemid particles (eluate 3). Eachfraction was diluted appropriately in 2YT media, mixed with fresh JM101,incubated at 37° C. for 5 minutes, and plated with 3 ml of 2YT soft agaron LB or LB carbenicillin plates.

Example IV Construction of hGH-Phagemid Particles with a Mixture of GeneIII Products

The gene III protein is composed of 410 residues divided into twodomains that are separated by a flexible linker sequence (Armstrong, J.,et al., FEBS Lett., 135:167-172, [1981]). The amino-terminal domain isrequired for attachment to the pili of E. coli, while thecarboxyl-terminal domain is imbedded in the phage coat and required forproper phage assembly (Crissman, J. W., Smith, G. P., Virology,132:445-455, [1984]). The signal sequence and amino-terminal domain ofgene III was replaced with the stlI signal and entire hGH gene (Chang etal. supra) by fusion to residue 198 in the carboxyl-terminal domain ofgene III (FIG. 1). The hGH-gene III fusion was placed under control ofthe lac promoter/operator in a plasmid (phGH-M13gIII; FIG. 1) containingthe pBR322 β-lactamase gene and Col E1 replication origin, and the phagef1 intergenic region. The vector can be easily maintained as a smallplasmid vector by selection on carbenicillin, which avoids relying on afunctional gene III fusion for propagation. Alternatively, the plasmidcan be efficiently packaged into virions (called phagemid particles) byinfection with helper phage such as M13KO7 (Viera et al. supra) whichavoids problems of phage assembly. Phagemid infectivity titers basedupon transduction to carbenicillin resistance in this system varied from2-5×10¹¹ colony forming units (cfu)/ml. The titer of the M13KO7 helperphage in these phagemid stocks is ˜10¹⁰ plaque forming units (pfu)/ml.

With this system we confirmed previous studies (Parmley, Smith supra)that homogeneous expression of large proteins fused to gene III isdeleterious to phage production (data not shown). For example, inductionof the lac promoter in phGH-M13gIII by addition of IPTG produced lowphagemid titers. Moreover, phagemid particles produced by co-infectionwith M13KO7 containing an amber mutation in gene III gave very lowphagemid titers (<10¹⁰ cfu/ml). We believed that multiple copies of thegene III fusion attached to the phagemid surface could lead to multiplepoint attachment (the “chelate effect”) of the fusion phage to theimmobilized target protein. Therefore to control the fusion protein copynumber we limited transcription of the hGH-gene III fusion by culturingthe plasmid in E. coli JM101 (lac^(Q)) which contains a constitutivelyhigh level of the lac repressor protein. The E. coli JM101 culturescontaining phGH-M13gIII were best propagated and infected with M13KO7 inthe absence of the lac operon inducer (IPTG); however, this system isflexible so that co-expression of other gene III fusion proteins can bebalanced. We estimate that about 10% of the phagemid particles containone copy of the hGH gene III fusion protein from the ratio of the amountof hGH per virion (based on hGH immuno-reactive material in CsClgradient purified phagemid). Therefore, the titer of fusion phagedisplaying the hGH gene III fusion is about 2-5×10¹⁰/ml. This number ismuch greater than the titer of E. coli (˜10⁸ to 10⁹/ml) in the culturefrom which they are derived. Thus, on average every E. coli cellproduces 10-100 copies of phage decorated with an hGH gene III fusionprotein.

Example V Structural Integrity of the hGH-Gene III Fusion

Immunoblot analysis (FIG. 2) of the hGH-gene III phagemid show that hGHcross-reactive material comigrates with phagemid particles in agarosegels. This indicates that the hGH is tightly associated with phagemidparticles. The hGH-gene III fusion protein from the phagemid particlesruns as a single immuno-stained band showing that there is littledegradation of the hGH when it is attached to gene III. Wild-type geneIII protein is clearly present because about 25% of the phagemidparticles are infectious. This is comparable to specific infectivityestimates made for wild-type M13 phage that are similarly purified (byCsCl density gradients) and concentrations estimated by UV absorbance(Smith, G. P. supra and Parmley, Smith supra) Thus, both wild-type geneIII and the hGH-gene III fusion proteins are displayed in the phagepool.

It was important to confirm that the tertiary structure of the displayedhGH was maintained in order to have confidence that results from bindingselections will translate to the native protein. We used monoclonalantibodies (Mabs) to hGH to evaluate the structural integrity of thedisplayed hGH gene III fusion protein (Table I). TABLE I Binding ofEight Different Monoclonal Antibodies (Mab's) to hGH and hGH PhagemidParticles* IC₅₀ (nM) Mab hGH hGH-phagemid 1 0.4 0.4 2 0.04 0.04 3 0.20.2 4 0.1 0.1 5 0.2 >2.0 6 0.07 0.2 7 0.1 0.1 8 0.1 0.1*Values given represent the concentration (nM) of hGH or hGH-phagemidparticles to give half-maximal binding to the particular Mab. Standarderrors in these measurements are typically at or below ±30% of thereported value.See Materials and Methods for further details.

The epitopes on hGH for these Mabs have been mapped (Cunningham et al.supra) and binding for 7 of 8 Mabs requires that hGH be properly folded.The IC₅₀ values for all Mabs were equivalent to wild-type hGH except forMab 5 and 6. Both Mabs 5 and 6 are known to have binding determinantsnear the carboxyl-terminus of hGH which is blocked in the gene IIIfusion protein. The relative IC₅₀ value for Mab1 which reacts with bothnative and denatured hGH is unchanged compared to the conformationallysensitive Mabs 2-5, 7 and 8. Thus, Mab1 serves as a good internalcontrol for any errors in matching the concentration of the hGH standardto that of the hGH-gene III fusion.

Example VI Binding Enrichments on Receptor Affinity Beads

Previous workers (Parmley, Smith supra; Scott, Smith supra; Cwirla etal. supra; and Devlin et al. supra) have fractionated phage by panningwith streptavidin coated polystyrene petri dishes or microtiter plates.However, chromatographic systems would allow more efficientfractionation of phagemid particles displaying mutant proteins withdifferent binding affinities. We chose non-porous oxirane beads. (Sigma)to avoid trapping of phagemid particles in the chromatographic resin.Furthermore, these beads have a small particle size (1 μm) to maximizethe surface area to mass ratio. The extracellular domain of the hGHreceptor (hGHbp) (Fuh et al., supra) containing a free cysteino residuewas efficiently coupled to these beads and phagemid particles showedvery low non-specific binding to beads coupled only to bovine serumalbumin (Table II). TABLE II Specific Binding of Hormone Phage tohGHbp-coated Beads Provides an Enrichment for hGH-phage over M13KO7Phage* Sample Absorbent^(‡) Total pfu Total cfu Ratio (cfu/pfu)Enrichment^(§) Original mixture^(†) 8.3 × 10¹¹ 2.9 × 10⁸ 3.5 × 10⁻⁴ (1)Supernatant BSA 7.4 × 10¹¹ 2.8 × 10⁸ 3.8 × 10⁻⁴ 1.1 hGHbp 7.6 × 10¹¹ 3.3× 10⁸ 4.3 × 10⁻⁴ 1.2 Wash 1 BSA 1.1 × 10¹⁰ 6.0 × 10⁶ 5.5 × 10⁻⁴ 1.6hGHbp 1.9 × 10¹⁰ 1.7 × 10⁷ 8.9 × 10⁻⁴ 2.5 Wash 2 BSA 5.9 × 10⁷ 2.8 × 10⁴4.7 × 10⁻⁴ 1.3 hGHbp 4.9 × 10⁷ 2.7 × 10⁶ 5.5 × 10⁻² 1.6 × 10² Eluate 1(hGH) BSA 1.1 × 10⁶ 1.9 × 10³ 1.7 × 10⁻³ 4.9 hGHbp 1.2 × 10⁶ 2.1 × 10⁶1.8 5.1 × 10³ Eluate 2 (hGH) BSA 5.9 × 10⁵ 1.2 × 10³ 2.0 × 10⁻³ 5.7hGHbp 5.5 × 10⁵ 1.3 × 10⁶ 2.4 6.9 × 10³ Eluate 3 (pH 2.1) BSA 4.6 × 10⁵2.0 × 10³ 4.3 × 10⁻³ 12.3  hGHbp 3.8 × 10⁵ 4.0 × 10⁶ 10.5  3.0 × 10⁴*The titers of M13KO7 and hGH-phagemid particles in each fraction wasdetermined by multiplying the number of plaque forming units (pfu) orcarbenicillin resistant colony forming units (cfu) by the dilutionfactor, respectively. See Example IV for details.^(†)The ratio of M13KO7 to hGH-phagemid particles was adjusted to 3000:1in the original mixture.^(‡)Absorbents were conjugated with BSA or hGHbp.^(§)Enrichments are calculated by dividing the cfu/pfu ratio after eachstep by cfu/pfu ratio in the original mixture.

In a typical enrichment experiment (Table II), one part of hGH phagemidwas mixed with >3,000 parts M13KO7 phage. After one cycle of binding andelution, 10⁶ phage were recovered and the ratio of phagemid to M13KO7phage was 2 to 1. Thus, a single binding selection step gave >5000-foldenrichment. Additional elutions with free hGH or acid treatment toremove remaining phagemids produced even greater enrichments. Theenrichments are comparable to those obtained by Smith and coworkersusing batch elution from coated polystyrene plates (Smith, G. P. supraand Parmely, Smith supra) however much smaller volumes are used on thebeads (200 μl vs. 6 ml). There was almost no enrichment for the hGHphagemid over M13KO7 when we used beads linked only to BSA. The slightenrichment observed for control beads (˜10-fold for pH 2.1 elution;Table 2) may result from trace contaminants of bovine growth hormonebinding protein present in the BSA linked to the bead. Neverthelessthese data show the enrichments for the hGH phage depend upon thepresence of the hGHbp on the bead suggesting binding occurs by specificinteraction between hGH and the hGHbp.

We evaluated the enrichment for wild-type hGH over a weaker bindingvariant of the hGH on fusion phagemids to further demonstrate enrichmentspecificity, and to link the reduction in binding affinity for thepurified hormones to enrichment factors after panning fusion phagemids.A fusion phagemid was constructed with an hGH mutant in which Arg64 wassubstituted with Ala (R64A). The R64A variant hormone is about 20-foldreduced in receptor binding affinity compared to hGH (Kd values of 7.1nM and 0.34 nM, respectively [Cunningham, Wells, supra]). The titers ofthe R64A hGH-gene III fusion phagemid were comparable to those ofwild-type hGH phagemid. After one round of binding and elution (TableIII) the wild-type hGH phagemid was enriched from a mixture of the twophagemids plus M13KO7 by 8-fold relative to the phagemid R64A, and ˜10⁴relative to M13KO7 helper phage. TABLE III hGHbp-coated Beads Select forhGH Phagemids Over a Weaker Binding hGH Variant Phagemid Control beadshGHbp beads WT phagemid enrichment WT phagemid enrichment Sample{overscore (total phagemid)} for WT/R64A {overscore (total phagemid)}for WT/R64A Original mixture 8/20 (1)    8/20 (1)   Supernatant ND — 4/10 1.0 Elution 1 (hGH) 7/20 0.8 17/20  8.5^(‡) Elution 2 (pH 2.1)11/20  1.8 21/27 5.2*The parent M13KO7 phage, wild-type hGH phagemid and R64A phagemidparticles were mixed at a ratio of 10⁴:0.4:0.6. Binding selections werecarried out using beads linked with BSA (control beads) or with thehGHbp (hGHbp beads) as described in Table II and the Materials andMethods After each step, plasmid DNA was isolated(Birnboim, H. C., Doly,J., Nucleic Acids Res., 7: 1513-1523, [1979]) from carbenicillinresistant colonies and# analyzed by restriction analysis to determine if it contained thewild-type hGH or the R64A hGH gene III fusion.^(†)The enrichment for wild-type hGH phagemid over R64A mutant wascalculated from the ratio of hGH phagemid present after each step tothat present in the original mixture (8/20), divided by thecorresponding ratio for R64A phagemids.WT = wild-type;ND = not determined.^(‡)The enrichment for phagemid over total M13KO7 parental phage was˜10⁴ after this step.

Conclusions

By displaying a mixture of wild-type gene III and the gene III fusionprotein on phagemid particles one can assemble and propagate virionsthat display a large and proper folded protein as a fusion to gene III.The copy number of the gene III fusion protein can be effectivelycontrolled to avoid “chelate effects” yet maintained at high enoughlevels in the, phagemid pool to permit panning of large epitopelibraries (>10¹⁰). We have shown that hGH (a 22 kD protein) can bedisplayed in its native folded form. Binding selections performed onreceptor affinity beads eluted with free hGH, efficiently enriched forwild-type hGH phagemids over a mutant hGH phagemid shown to have reducedreceptor binding affinity. Thus, it is possible to sort phagemidparticles whose binding constants are down in the nanomolar range.

Protein-protein and antibody-antigen interactions are dominated bydiscontinuous epitopes (Janin, J., et al., J. Mol. Biol., 204:155-164,[1988]; Argos, P., Prot. Eng., 2:101-113, [1988]; Barlow, D. J., et al.,Nature, 322:747-748, [1987]; and Davies, D. R., et al., J. Biol. Chem.,263:10541-10544, [1988]); that is the residues directly involved inbinding are close in tertiary structure but separated by residues notinvolved in binding. The screening system presented here should allowone to analyze more conveniently protein-receptor interactions andisolate discontinuous epitopes in proteins with new and high affinitybinding properties.

Example VII Selection of hGH Mutants from a Library Randomized at hGHCodons 172, 174, 176, 178

Construction of Template

A mutant of the hGH-gene III fusion protein was constructed using themethod of Kunkel., et al. Meth. Enzymol. 154, 367-382 [1987]. TemplateDNA was prepared by growing the plasmid pS0132 (containing the naturalhGH gene fused to the carboxy-terminal half of M13 gene III, undercontrol of the alkaline phosphatase promoter) in CJ236 cells withM13-K07 phage added as helper. Single-stranded, uracil-containing DNAwas prepared for mutagenesis to introduce (1) a mutation in hGH whichwould greatly reduce binding to the hGH binding protein (hGHbp); and (2)a unique restriction site (KpnI) which could be used for assayingfor—and selecting against—parental background phage.Oligonucleotide-directed mutagenesis was carried out using T7 DNApolymerase and the following oligodeoxy-nucleotide (SEQ ID NO:7):                             Gly Thr hGH codon:                   178179             5′-G ACA TTC CTG GGT ACC GTG CAG T-3′                          < KpnI >This oligo introduces the KpnI site as shown, along with mutations(R178G, I179T) in hGH. These mutations are predicted to reduce bindingof hGH to hGHbp by more than 30-fold. Clones from the mutagenesis werescreened by KpnI digestion and confirmed by dideoxy DNA sequencing. Theresulting construct, to be used as a template for random mutagenesis,was designated pHO415.Random Mutagenesis within Helix-4 of hGH

Codons 172, 174, 176, 178 were targeted for random mutagenesis in hGH,again using the method of Kunkel. Single-stranded template from pH0415was prepared as above and mutagenesis was carried out using thefollowing pool of oligos (SEQ ID NO:8): hGHcodon:                        172     174   5′-  GC TTC AGG AAG GAC ATGGAC NNS GTC NNS ACA-                   Ile       176     178 179    - NNS CTG NNS ATC GTG CAG TGC CGC TCT GTG G-3′As shown, this oligo pool reverts codon 179 to wild-type (IIe), destroysthe unique KpnI site of pH0415, and introduces random codons (NNS, whereN=A,G,C, or T and S=G or C) at positions 172, 174, 176, and 178. Usingthis codon selection in the context of the above sequence, no additionalKpnI sites can be created. The choice of the NNS degenerate sequenceyields 32 possible codons (including one “stop” codon, and at least onecodon for each amino acid) at 4 sites, for a total of (32)⁴=1,048,576possible nucleotide sequences (12% of which contain at least one stopcodon), or (20)⁴=160,000 possible polypeptide sequences plus 34,481prematurely terminated sequences (i.e. sequences containing at least onestop codon).Propagation of the Initial Library

The mutagenesis products were extracted twice with phenol:chloroform(50:50) and ethanol precipitated with an excess of carrier tRNA to avoidadding salt that would confound the subsequent electroporation step.Approximately 50 ng (15 fmols) of DNA was electroporated into WJM101cells (2.8×10¹⁰ cells/mL) in 45 μL total volume in a 0.2 cm cuvette at avoltage setting of 2.49 kV with a single pulse (time constant=4.7msec.).

The cells were allowed to recover 1 hour at 37° C. with shaking, thenmixed with 25 mL 2YT medium, 100 μg/mL carbenicillin, and M13-K07(multiplicity of infection=1000). Plating of serial dilutions from thisculture on carbenicillin-containing media indicated that 8.2×10⁶electrotransformants were obtained. After 10′ at 23° C., the culture wasincubated overnight (15 hours) at 37° C. with shaking.

After overnight incubation, the cells were pelleted, and double-strandedDNA (dsDNA), designated pLIB1, was prepared by the alkaline lysismethod. The supernatant was spun again to remove any remaining cells,and the phage, designated phage pool φ1, were PEG-precipitated andresuspended in 1 mL STE buffer (10 mM Tris, pH 7.6, 1 mM EDTA, 50 mMNaCl). Phage titers were measured as colony-forming units (CFU) for therecombinant phagemid containing hGH-g3p gene III fusion (hGH-g³)plasmid, and plaque-forming units (PFU) for the M13-K07 helper phage.

Binding Selection Using Immobilized hGHbp

1. BINDING: An aliquot of phage pool φ1 (6×10⁹ CFU, 6×10⁷ PFU) wasdiluted 4.5-fold in buffer A (Phosphate-buffered saline, 0.5% BSA, 0.05%Tween-20, 0.01% thimerosal) and mixed with a 5 μL suspension ofoxirane-polyacrylamide beads coupled to the hGHbp containing a Ser237Cys mutation (350 fmols) in a 1.5 mL silated polypropylene tube. As acontrol, an equivalent aliquot of phage were mixed in a separate tubewith beads that had been coated with BSA only. The phage were allowed tobind to the beads by incubating 3 hours at room temperature (23° C.)with slow rotation (approximately 7 RPM). Subsequent steps were carriedout with a constant volume of 200 μL and at room temperature.

2. WASH: The beads were spun 15 sec., and the supernatant was removed(Sup. 1). To remove phage/phagemid not specifically bound, the beadswere washed twice by resuspending in buffer A, then pelleting. A finalwash consisted of rotating the beads in buffer A for 2 hours.

3. hGH ELUTION: Phage/phagemid binding weakly to the beads were removedby stepwise elution with hGH. In the first step, the beads were rotatedwith buffer A containing 2 nM hGH. After 17 hours, the beads werepelleted and resuspended in buffer A containing 20 nM hGH and rotatedfor 3 hours, then pelleted. In the final hGH wash, the beads weresuspended in buffer A containing 200 nM hGH and rotated for 3 hours thenpelleted.

4. GLYCINE ELUTION: To remove the tightest-binding phagemid (i.e. thosestill bound after the hGH washes), beads were suspended in Glycinebuffer (1 M Glycine, pH 2.0 with HCl), rotated 2 hours and pelleted. Thesupernatant (fraction “G”; 200 μL) was neutralized by adding 30 μL of 1M Tris base.

Fraction G eluted from the hGHbp-beads (1×10⁶ CFU, 5×10⁴ PFU) was notsubstantially enriched for phagemid over K07 helper phage. We believethis resulted from the fact that K07 phage packaged during propagationof the recombinant phagemid display the hGH-g3p fusion.

However, when compared with fraction G eluted from the BSA-coatedcontrol beads, the hGHbp-beads yielded 14 times as many CFU's. Thisreflects the enrichment of tight-binding hGH-displaying phagemid overnonspecifically-binding phagemid.

5. PROPAGATION: An aliquot (4.3×10⁵ CFU) of fraction G eluted from thehGHbp-beads was used to infect log-phase WJM101 cells. Transductionswere carried out by mixing 100 μL fraction G with 1 mL WJM101 cells,incubating 20 min. at 37° C., then adding K07 (multiplicity ofinfection=1000). Cultures (25 mL 2YT plus carbenicillin) were grown asdescribed above and the second pool of phage (Library 1G, for firstglycine elution) were prepared as described above.

Phage from library 1G (FIG. 3) were selected for binding to hGHbp beadsas described above. Fraction G eluted from hGHbp beads contained 30times as many CFU's as fraction G eluted from BSA-beads in thisselection. Again, an aliquot of fraction G was propagated in WJM101cells to yield library 1G² (indicating that this library had been twiceselected by glycine elution). Double-stranded DNA (pLIB 1G²) was alsoprepared from this culture.

KpnI Assay and Restriction-Selection of dsDNA

To reduce the level of background (KpnI⁺) template, an aliquot (about0.5 μg) of pLIB 1G² was digested with KpnI and electroporated intoWJM101 cells. These cells were grown in the presence of K07(multiplicity of infection=100) as described for the initial library,and a new phage pool, pLIB 3, was prepared (FIG. 3).

In addition, an aliquot (about 0.5 μg) of dsDNA from the initial library(pLIB1) was digested with KpnI and electroporated directly into WJM101cells. Transformants were allowed to recover as above, infected withM13-K07, and grown overnight to obtain a new library of phage,designated phage Library 2 (FIG. 3).

Successive Rounds of Selection

Phagemid binding, elution, and propagation were carried out insuccessive rounds for phagemid derived from both pLIB 2 and pLIB 3 (FIG.3) as described above, except that (1) an excess (10-fold over CFU) ofpurified K07 phage (not displaying hGH) was added in the bead-bindingcocktail, and (2) the hGH stepwise elutions were replaced with briefwashings of buffer A alone. Also, in some cases, XL1-Blue cells wereused for phagemid propagation.

An additional digestion of dsDNA with KpnI was carried out on pLIB 2G³and on pLIB 3G⁵ before the final round of bead-binding selection (FIG.3).

DNA Sequencing of Selected Phagemids

Four independently isolated clones from LIB 4G⁴ and four independentlyisolated clones from LIB 5G⁶ were sequenced by dideoxy sequencing. Alleight of these clones had identical DNA sequences (SEQ ID NO:9): hGHcodon:    172     174     176     178           5′ -AAG GTC TCC ACA TACCTG AGG ATC-3′Thus, all these encode the same mutant of hGH: (E174S, F176Y). Residue172 in these clones is Lys as in wild-type. The codon selected for 172is also identical to wild-type hGH. This is not surprising since AAG isthe only lysine-codon possible from a degenerate “NNS” codon set.Residue 178-Arg is also the same as wild-type, but here, the codonselected from the library was AAG instead of CGC as is found inwild-type hGH, even though the latter codon is also possible using the“NNS” codon set.Multiplicity of K07 Infection

The multiplicity of infection of K07 infection is an important parameterin the propagation of recombinant phagemids. The K07 multiplicity ofinfection must be high enough to insure that virtually all cellstransformed or transfected with phagemid are able to package newphagemid particles. Furthermore, the concentration of wild-type gene IIIin each cell should be kept high to reduce the possibility of multiplehGH-gene III fusion molecules being displayed on each phagemid particle,thereby reducing chelate effects in binding. However, if the K07multiplicity of infection is too high, the packaging of K07 will competewith that of recombinant phagemid. We find that acceptable phagemidyields, with only 1-10% background K07 phage, are obtained when the K07multiplicity of infection is 100. TABLE IV Enrichment hGHbp/BSA PhagePool moi (K07) CFU/PFU beads Fraction Kpnl LIB 1 1000 ND 14 0.44 LIB 1G1000 ND 30 0.57 LIB 3 100 ND 1.7 0.26 LIB 3G³ 10 ND 8.5 0.18 LIB 3G⁴ 100460 220 0.13 LIB 5 100 ND 15 ND LIB 2 100 ND 1.7 <0.05 LIB 2G 10 ND 4.1<0.10 LIB 2G² 100 1000  27 0.18 LIB 4 100 170 38 ND

Phage pools are labelled as shown (FIG. 3). The multiplicity ofinfection (moi) refers to the multiplicity of K07 infection (PFU/cells)in the propagation of phagemid. The enrichment of CFU over PFU is shownin those cases where purified K07 was added in the binding step. Theratio of CFU eluting from hGHbp-beads over CFU eluting from BSA-beads isshown. The fraction of KpnI-containing template (i.e., pH0415) remainingin the pool was determined by digesting dsDNA with KpnI plus EcoRI,running the products on a 1% agarose gel, and laser-scanning a negativeof the ethidium bromide-stained DNA.

Receptor-Binding Affinity of the Hormone hGH(E174S, F176Y)

The fact that a single clone was isolated from two different pathways ofselection (FIG. 3) suggested that the double mutant (E174S,F176Y) bindsstrongly to hGHbp. To determine the affinity of this mutant of hGH forhGHbp, we constructed this mutant of hGH by site-directed mutagenesis,using a plasmid (pB0720) which contains the wild-type hGH gene astemplate and the following oligonucleotide which changes codons 174 and176 (SEQ ID NO:10): hGH codon:  172     174     176     178            Lys     Ser     Tyr     Arg 5′- ATG GAC AAG GTG TCG ACA TACCTG CGC ATC GTG -3′The resulting construct, pH0458B, was transformed into E. coli strain16C9 for expression of the mutant hormone. Scatchard analysis ofcompetitive binding of hGH(E174S,F176Y) versus ¹²⁵I-hGH to hGHbpindicated that the (E174S,F176Y) mutant has a binding affinity at least5.0-fold tighter than that of wild-type hGH.

Example VIII Selection of hGH Variants from a Helix-4 Random CassetteLibrary of Hormone-Phage

Human growth hormone variants were produced by the method of the presentinvention using the phagemid described in FIG. 9.

Construction of a De-Fusable Hormone-Phage Vector

We designed a vector for cassette mutagenesis (Wells et al., Gene 34,315-323 [1985]) and expression of the hGH-gene III fusion protein withthe objectives of (1) improving the linkage between hGH and the gene IIImoiety to more favorably display the hGH moiety on the phage (2)limiting expression of the fusion protein to obtain essentially“monovalent display,” (3) allowing for restriction nuclease selectionagainst the starting vector, (4) eliminating expression of fusionprotein from the starting vector, and (5) achieving facile expression ofthe corresponding free hormone from a given hGH-gene III fusion mutant.

Plasmid pS0643 was constructed by oligonucleotide-directed mutagenesis(Kunkel et al., Methods Enzymol. 154, 367-382 [1987]) of pS0132, whichcontains pBR322 and f1 origins of replication and expresses an hGH-geneIII fusion protein (hGH residues 1-191, followed by a single Glyresidue, fused to Pro-198 of gene III) under the control of the E. coliphoA promoter (Bass et al., Proteins 8, 309-314 [1990])(FIG. 9).Mutagenesis was carried out with the oligonucleotide5′-GGC-AGC-TGT-GGC-TTC-TAG-AGT-GGC-GGC-GGC-TCT-GGT-3′ (SEQ ID NO:1),which introduces a XbaI site (underlined) and an amber stop codon (TAG)following Phe-191 of hGH. In the resulting construct, pS0643, a portionof gene III was deleted, and two silent mutations (underlined) occurred,yielding the following junction between hGH and gene III (SEQ ID NOS: 11AND 12): --- hGH ---->            gene III----> 187 188 189 190 191 am*249 250 251 252 253 254 Gly Ser Cys Gly Phe Glu Ser Gly Gly Gly Ser GlyGGC AGC TGT GG A  TTC TAG AGT GG C  GGT GGC TCT GGT

This shortens the total size of the fusion protein from 401 residues inpS0132 to 350 residues in pS0643. Experiments using monoclonalantibodies against hGH have demonstrated that the hGH portion of the newfusion protein, assembled on a phage particle, is more accessible thanwas the previous, longer fusion.

For propagation of hormone-displaying phage, pS0643 and derivatives canbe grown in a amber-suppressor strain of E. coli, such as JM101 orXL1-Blue (Bullock et al., BioTechniques 5, 376-379 [1987]). Shown aboveis substitution of Glu at the amber codon which occurs in supEsuppressor strains. Suppression with other amino acids is also possiblein various available strains of E. coli well known and publicallyavailable.

To express hGH (or mutants) free of the gene III portion of the fusion,pS0643 and derivatives can simply be grown in a non-suppressor strainsuch as 16C9. In this case, the amber codon (TAG) leads to terminationof translation, which yields free hormone, without the need for anindependent DNA construction.

To create sites for cassette mutagenesis, pS0643 was mutated with theoligonucleotides (1) 5′-CGG-ACT-GGG-CAG-ATA-TTC-AAG-CAG-ACC-3′ (SEQ IDNO:13), which destroys the unique BgIII site of pS0643; (2)5′-CTC-AAG-AAC-TAC-GGG-TTA-CCC-TGA-CTG-CTT-CAG-GM-GG-3′ (SEQ ID NO:14),which inserts a unique BstEII site, a single-base frameshift, and anon-amber stop codon (TGA); and (3)5′-CGC-ATC-GTG-CAG-TGC-AGA-TCT-GTG-GAG-GGC-3′ (SEQ ID NO:15), whichintroduces a new BgIII site, to yield the starting vector, pH0509. Theaddition of a frameshift along with a TGA stop codon insures that nogeneIII-fusion can be produced from the starting vector. TheBstEII-BgIII segment is cut out of pH0509 and replaced with a DNAcassette, mutated at the codons of interest. Other restriction sites forcassette mutagenesis at other locations in hGH have also been introducedinto the hormone-phage vector.

Cassette Mutagenesis within Helix 4 of hGH

Codons 172, 174, 176 and 178 of hGH were targeted for random mutagenesisbecause they all lie on or near the surface of hGH and contributesignificantly to receptor-binding (Cunningham and Wells, Science 244,1081-1085 [1989]); they all lie within a well-defined structure,occupying 2 “turns” on the same side of helix 4; and they are eachsubstituted by at least one amino acid among known evolutionary variantsof hGH.

We chose to substitute NNS (N=A/G/C/T; S=G/C) at each of the targetresidues. The choice of the NNS degenerate sequence yields 32 possiblecodons (including at least one codon for each amino acid) at 4 sites,for a total of (32)⁴=1,048,576 possible nucleotide sequences, or(20)⁴=160,000 possible polypeptide sequences. Only one stop codon, amber(TAG), is allowed by this choice of codons, and this codon issuppressible as Glu in supE strains of E. coli.

Two degenerate oligonucleotides, with NNS at codons 172, 174, 176, and178, were synthesized, phosphorylated, and annealed to construct themutagenic cassette:5′-GT-TAC-TCT-ACT-GCT-TTC-AGG-AAG-GAC-ATG-GAC-NNS-GTC-NNS-ACA-NNS-CTG-NNS-ATC-GTG-CAG-TGC-A-3′(SEQ ID NO:16), and5′-GA-TCT-GCA-CTG-CAC-GAT-SNN-CAG-SNN-TGT-SNN-GAC-SNN-GTC-CAT-GTC-CTT-CCT-GAA-GCA-GTA-GA-3′(SEQ ID NO:17).

The vector was prepared by digesting pH0509 with BstEII followed byBgIII. The products were run on a 1% agarose gel and the large fragmentexcised, phenol-extracted, and ethanol precipitated. This fragment wastreated with calf intestinal phosphatase (Boehringer), thenphenol:chloroform extracted, ethanol precipitated, and resuspended forligation with the mutagenic cassette.

Propagation of the Initial Library in XL1-Blue Cells

Following ligation, the reaction products were again digested withBstEII, then phenol:chloroform extracted, ethanol precipitated andresuspended in water. (A BstEII recognition site (GGTNACC) is createdwithin cassettes which contain a G at position 3 of codon 172 and an ACC(Thr) codon at 174. However, treatment with BstEII at this step shouldnot select against any of the possible mutagenic cassettes, becausevirtually all cassettes will be heteroduplexes, which cannot be cleavedby the enzyme.) Approximately 150 ng (45 fmols) of DNA waselectroporated into XL1-Blue cells (1.8×10⁹ cells in 0.045 mL) in a 0.2cm cuvette at a voltage setting of 2.49 kV with a single pulse (timeconstant=4.7 msec.).

The cells were allowed to recover 1 hour at 37° C. in S.O.C media withshaking, then mixed with 25 mL 2YT medium, 100 mg/mL carbenicillin, andM13-K07 (moi=100). After 10′ at 23° C., the culture was incubatedovernight (15 hours) at 37° C. with shaking. Plating of serial dilutionsfrom this culture onto carbenicillin-containing media indicated that3.9×10⁷ electrotransformants were obtained.

After overnight incubation, the cells were pelleted, and double-strandedDNA (dsDNA), designated pH0529E (the initial library), was prepared bythe alkaline lysis method. The supernatant was spun again to remove anyremaining cells, and the phage, designated phage pool φH0529E (theinitial library of phage), were PEG-precipitated and resuspended in 1 mLSTE buffer (10 mM Tris, pH 7.6, 1 mM EDTA, 50 mM NaCl). Phage titerswere measured as colony-forming units (CFU) for the recombinant phagemidcontaining hGH-g3p. Approximately 4.5×10¹³ CFU were obtained from thestarting library.

Degeneracy of the Starting Library

From the pool of electrotransformants, 58 clones were sequenced in theregion of the BstEII-BgIII cassette. Of these, 17% corresponded to thestarting vector, 17% contained at least one frame shift, and 7%contained a non-silent (non-terminating) mutation outside the fourtarget codons. We conclude that 41% of the clones were defective by oneof the above measures, leaving a total functional pool of 2.0×10⁷initial transformants. This number still exceeds the possible number ofDNA sequences by nearly 20-fold. Therefore, we are confident of havingall possible sequences represented in the starting library.

We examined the sequences of non-selected phage to evaluate the degreeof codon bias in the mutagenesis (Table V). The results indicated that,although some codons (and amino acids) are under- or over-representedrelative to the random expectation, the library is extremely diverse,with no evidence of large-scale “sibling” degeneracy (Table VI). TABLE VCodon distribution (per 188 codons) of non-selected hormone phage.Clones were sequenced from the starting library (pH0529E). All codonswere tabulated, including those from clones which contained spuriousmutations and/or frameshifts. Residue Number expected Number foundFound/Expected Leu 17.6 18 1.0 Ser 17.6 26 1.5 Arg 17.6 10 0.57 Pro 11.816 1.4 Thr 11.8 14 1.2 Ala 11.8 13 1.1 Gly 11.8 16 1.4 Val 11.8 4 0.3Ile 5.9 2 0.3 Met 5.9 1 0.2 Tyr 5.9 1 0.2 His 5.9 2 0.3 Trp 5.9 2 0.3Phe 5.9 5 0.9 Cys 5.9 5 0.9 Gln 5.9 7 1.2 Asn 5.9 14 2.4 Lys 5.9 11 1.9Asp 5.9 9 1.5 Glu 5.9 6 1.0 amber* 5.9 6 1.0*Note: the amber stop codon (TAG) is suppressed as Glu in XL1-Bluecells. Highlighted codons were over/under-represented by 50% or more.

TABLE VI Non-selected (pH0529E) clones with an open reading frame. Thenotation, e.g. TWGS, denotes the hGH mutant 172T/174W/176G/178S. Amber(TAG) codons, translated as Glu in XL1-Blue cells are shown as ε.KεNT (SEQ ID NO:46) TWGS (SEQ ID NO:47) PεER (SEQ ID NO:48) LPPS (SEQ IDNO:49) SLDP (SEQ ID NO:50) QQSN (SEQ ID NO:51) GSKT (SEQ ID NO:52)TPVT (SEQ ID NO:53) RSRA (SEQ ID NO:54) LCGL (SEQ ID NO:55) TGRL (SEQ IDNO:56) AKAS (SEQ ID NO:57) GNDD (SEQ ID NO:58) KTEQ (SEQ ID NO:59)NNCR (SEQ ID NO:60) FPCL (SEQ ID NO:61) NSDF (SEQ ID NO:62) HRPS (SEQ IDNO:63) LSLε (SEQ ID NO:64) NGSK (SEQ ID NO:65) LTTE (SEQ ID NO:66)PSGG (SEQ ID NO:67) LWFP (SEQ ID NO:68) PAGS (SEQ ID NO:69) GRAK (SEQ IDNO:70) GTNG (SEQ ID NO:71) CVLQ (SEQ ID NO:72) EASL (SEQ ID NO:73)SSKE (SEQ ID NO:74) ALLL (SEQ ID NO:75) PSHP (SEQ ID NO:76) SYAP (SEQ IDNO:77) ASNG (SEQ ID NO:78) EANN (SEQ ID NO:79) KNAK (SEQ ID NO:80)SRGK (SEQ ID NO:81) GLDG (SEQ ID ND:82) NDPI (SEQ ID NO:83)Preparation of Immobilized hGHbp and hPRLbp

Immobilized hGHbp (“hGHbp-beads”) was prepared as described (Bass etal., Proteins 8, 309-314 [1990]), except that wild-type hGHbp (Fuh etal., J. Biol. Chem. 265, 3111-3115 [1990]) was used. Competitive bindingexperiments with [¹²⁵I] hGH indicated that 58 fmols of functional hGHbpwere coupled per μL of bead suspension.

Immobilized hPRLbp (“hPRLbp-beads”) was prepared as above, using the211-residue extracellular domain of the prolactin receptor (Cunninghamet al., Science 250, 1709-1712 [1990]). Competitive binding experimentswith [¹²⁵I] hGH in the presence of 50 μM zinc indicated that 2.1 fmolsof functional hPRLbp were coupled per μL of bead suspension.

“Blank beads” were prepared by treating the oxirane-acrylamide beadswith 0.6 M ethanolamine (pH 9.2) for 15 hours at 4° C.

Binding Selection Using Immobilized hGHbp and hPRLbp

Binding of hormone-phage to beads was carried out in one of thefollowing buffers: Buffer A (PBS, 0.5% BSA, 0.05% Tween 20, 0.01%thimerosal) for selections using hGHbp and blank beads; Buffer B (50 mMtris pH 7.5, 10 mM MgCl₂, 0.5% BSA, 0.05% Tween 20, 100 mM ZnC₂) forselections using hPRLbp in the presence of zinc (+Zn²⁺); or Buffer C(PBS, 0.5% BSA, 0.05% Tween 20, 0.01% thimerosal, 10 mM EDTA) forselections using hPRLbp in the absence of zinc (+EDTA). Bindingselections were carried out according to each of the following paths:(1) binding to blank beads, (2) binding to hGHbp-beads, (3) binding tohPRLbp-beads (+Zn²⁺), (4) binding to hPRLbp-beads (+EDTA), (5)pre-adsorbing twice with hGHbp beads then binding the non-adsorbedfraction to hPRLbp-beads (“−hGHbp, +hPRLbp” selection), or (6)pre-adsorbing twice with hPRLbp-beads then binding the non-adsorbedfraction to hGHbp-beads (“−hPRLbp, +hGHbp” selection). The latter twoprocedures are expected to enrich for mutants binding hPRLbp but nothGHbp, or for mutants binding hGHbp but not hPRLbp, respectively.Binding and elution of phage was carried out in each cycle as follows:

1. BINDING: An aliquot of hormone phage (typically 10⁹-10¹⁰ CFU) wasmixed-with an equal amount of non-hormone phage (pCAT), diluted into theappropriate buffer (A, B, or C), and mixed with a 10 mL suspension ofhGHbp, hPRLbp or blank beads in a total volume of 200 mL in a 1.5 mLpolypropylene tube. The phage were allowed to bind to the beads byincubating 1 hour at room temperature (23° C.) with slow rotation(approximately 7 RPM). Subsequent steps were carried out with a constantvolume of 200 μL and at room temperature.

2. WASHES: The beads were spun 15 sec., and the supernatant was removed.To reduce the number of phage not specifically bound, the beads werewashed 5 times by resuspending briefly in the appropriate buffer, thenpelleting.

3. hGH ELUTION: Phage binding weakly to the beads were removed byelution with hGH. The beads were rotated with the appropriate buffercontaining 400 nM hGH for 15-17 hours. The supernatant was saved as the“hGH elution” and the beads. The beads were washed by resuspendingbriefly in buffer and pelleting.

4. GLYCINE ELUTION: To remove the tightest-binding phage (i.e. thosestill bound after the hGH wash), beads were suspended in Glycine buffer(Buffer A plus 0.2 M Glycine, pH 2.0 with HCl), rotated 1 hour andpelleted. The supernatant (“Glycine elution”; 200 μL) was neutralized byadding 30 mL of 1 M Tris base and stored at 4° C.

5. PROPAGATION: Aliquots from the hGH elutions and from the Glycineelutions from each set of beads under each set of conditions were usedto infect separate cultures of log-phase XL1-Blue cells. Transductionswere carried out by mixing phage with 1 mL XL1-Blue cells, incubating 20min. at 37° C., then adding K07 (moi=100). Cultures (25 mL 2YT pluscarbenicillin) were grown as described above and the next pool of phagewas prepared as described above.

Phage binding, elution, and propagation were carried out in successiverounds, according to the cycle described above. For example, the phageamplified from the hGH elution from hGHbp-beads were again selected onhGHbp-beads and eluted with hGH, then used to infect a new culture ofXL1-Blue cells. Three to five rounds of selection and propagation werecarried out for each of the selection procedures described above.

DNA Sequencing of Selected Phagemids

From the hGH and Glycine elution steps of each cycle, an aliquot ofphage-was used to inoculate XL1-Blue cells, which were plated on LBmedia containing carbenicillin and tetracycline to obtain independentclones from each phage pool. Single-stranded DNA was prepared fromisolated colony and sequenced in the region of the mutagenic cassette.The results of DNA sequencing are summarized in terms of the deducedamino acid sequences in FIGS. 5, 6, 7, and 8.

Expression and Assay of hGH Mutants

To determine the binding affinity of some of the selected hGH mutantsfor the hGHbp, we transformed DNA from sequenced clones into E. colistrain 16C9. As described above, this is a non-suppressor strain whichterminates translation of protein after the final Phe-191 residue ofhGH. Single-stranded DNA was used for these transformations, butdouble-stranded DNA or even whole phage can be easily electroporatedinto a non-suppressor strain for expression of free hormone.

Mutants of hGH were prepared from osmotically shocked cells by ammoniumsulfate precipitation as described for hGH (Olson et al., Nature 293,408-411 [1981]), and protein concentrations were measured by laserdensitomoetry of Coomassie-stained SDS-polyacrylamide gelelectrophoresis gels, using hGH as standard (Cunningham and Wells,Science 244,1081-1085 [1989]).

The binding affinity of each mutant was determined by displacement of¹²⁵I hGH as described (Spencer et al., J. Biol. Chem. 263, 7862-7867[1988]; Fuh et al., J. Biol. Chem. 265, 3111-3115 [1990]), using ananti-receptor monoclonal antibody (Mab263).

The results for a number of hGH mutants, selected by different pathways(FIG. 6) are shown in Table VII. Many of these mutants have a tighterbinding affinity for hGHbp than wild-type hGH. The most improved mutant,KSYR (SEQ ID NO:84), has a binding affinity 5.6 times greater than thatof wild-type hGH. The weakest selected mutant, among those assayed wasonly about 10-fold lower in binding affinity than hGH.

Binding assays may be carried out for mutants selected forhPRLbp-binding. TABLE VII Competitive binding to hGHbp The selected poolin which each mutant was found is indicated as 1G (first glycineselection), 3G (third glycine selection), 3H (third hGH selec- tion), 3*(third selection, not binding to hPRLbp, but binding to hGHbp). Thenumber of times each mutant occurred among all sequenced clones is shown( ) Kd(mut)/ Mutant Kd (nM) Kd(hGH) Pool KSYR (6) (SEQ ID NO:84) 0.06+ 0.01 0.18 1G,3G RSFR     (SEQ ID NO:85) 0.10 + 0.05 0.30 3GRAYR     (SEQ ID NO:86) 0.13 + 0.04 0.37 3* KTYK (2) (SEQ ID NO:87) 0.16+ 0.04 0.47 H,3G RSYR (3) (SEQ ID NO:88) 0.20 + 0.07 0.58 1G,3H, 3G KAYR(3) (SEQ ID NO:89) 0.22 + 0.03 0.66 3G RFFR (2) (SEQ ID NO:90) 0.26+ 0.05 0.76 3H KQYR     (SEQ ID NO:91) 0.33 + 0.03 1.0 3G KEFR = wt (9)0.34 + 0.05 1.0 3H,3G, 3* RTYH     (SEQ ID NO:92) 0.68 + 0.17 2.0 3HQRYR     (SEQ ID NO:93) 0.83 + 0.14 2.5 3* KKYK     (SEQ ID NO:94)  1.1+ 0.4  3.2 3* RSFS (2) (SEQ ID NO:95)  1.1 + 0.2  3.3 3G,* KSNR     (SEQID NO:96)  3.1 + 0.4  9.2 3*Additive and Non-Additive Effects on Binding

At some residues, substitution of a particular amino acid hasessentially the same effect independent of surrounding residues. Forexample, substitution of F176Y in the background of 172R/174S reducesbinding affinity by 2.0-fold (RSFR (SEQ ID NO:85) vs. RSYR (SEQ IDNO:88)). Similarly, in the background of 172K/174A the binding affinityof the F176Y mutant (KAYR (SEQ ID NO:89)) is 2.9-fold weaker than thecorresponding 176F mutant (KAFR; Cunningham and Wells, 1989).

On the other hand, the binding constants determined for several selectedmutants of hGH demonstrate non-additive effects of some amino acidsubstitutions at residues 172, 174, 176, and 178. For example, in thebackground of 172K/176Y, the substitution E174S results in a mutant(KSYR (SEQ ID NO:84)) which binds hGHbp 3.7-fold tighter than thecorresponding mutant containing E174A (KAYR (SEQ ID NO:89)). However, inthe background of 172R/176Y, the effects of these E174 substitutions arereversed. Here, the E174A mutant (RAYR (SEQ ID NO:86)) binds 1.5-foldtighter than the E174S mutant (RSYR (SEQ ID NO:88)).

Such non-additive effects on binding for substitutions at proximalresidues illustrate the utility of protein-phage binding selection as ameans of selecting optimized mutants from a library randomized atseveral positions. In the absence of detailed structural information,without such a selection process, many combinations of substitutionsmight be tried before finding the optimum mutant.

Example IX Selection of hGH Variants from a Helix-1 Random CassetteLibrary of Hormone-Phage

Using the methods described in Example VIII, we targeted another regionof hGH involved in binding to the hGHbp and/or hPRLbp, helix 1 residues10, 14, 18, 21, for random mutagenesis in the phGHam-g3p vector (alsoknown as pS0643; see Example VIII).

We chose to use the “amber” hGH-g3 construct (called phGHam-g3p) becauseit appears to make the target protein, hGH, more accessible for binding.This is supported by data from comparative ELISA assays of monoclonalantibody binding. Phage produced from both pS0132 (S. Bass, R. Greene,J. A. Wells, Proteins 8, 309 (1990).) and phGHam-g3 were tested withthree antibodies (Medix 2, 1B5.G2, and 5B7.C10) that are known to havebinding determinants near the carboxyl-terminus of hGH [B. C.Cunningham, P. Jhurani, P. Ng, J. A. Wells, Science 243, 1330 (1989); B.C. Cunningham and J. A. Wells, Science 244, 1081 (1989); L. Jin and J.Wells, unpublished results], and one antibody (Medix 1) that recognizesdeterminants in helices 1 and 3 ([B. C. Cunningham, P. Jhurani, P. Ng,J. A. Wells, Science 243, 1330 (1989); B. C. Cunningham and J. A. Wells,Science 244, 1081 (1989)]). Phagemid particles from phGHam-g3 reactedmuch more strongly with antibodies Medix 2, 1B5.G2, and 5B7.C10 than didphagemid particles from pS0132. In particular, binding of pS0132particles was reduced by >2000-fold for both Medix 2 and 5B7.C10 andreduced by >25-fold for 1B5.G2 compared to binding to Medix 1. On theother hand, binding of phGHam-g3 phage was weaker by only about1.5-fold, 1.2-fold, and 2.3-fold for the Medix 2, 1 B5.G2, and 5B7.C10antibodies, respectively, compared with binding to MEDIX 1.

Construction of the Helix 1 Library by Cassette Mutagenesis

We mutated residues in helix 1 that were previously identified byalanine-scanning mutagenesis [B. C. Cunningham, P. Jhurani, P. Ng, J. A.Wells, Science 243, 1330 (1989); B. C. Cunningham and J. A. Wells,Science 244, 1081 (1989), 15, 16) to modulate the binding of theextracellular domains of the hGH and/or hPRL receptors (called hGHbp andhPRLbp, respectively). Cassette mutagenesis was carried out essentiallyas described [J. A. Wells, M. Vasser, D. B. Powers, Gene 34, 315(1985)]. This library was constructed by cassette mutagenesis that fullymutated four residues at a time (see Example VIII) which utilized amutated version of phGHam-g3 into which unique KpnI (at hGH codon 27)andXhoI (at hGH codon 6) restriction sites (underlined below) had beeninserted by mutagenesis [T. A. Kunkel, J. D. Roberts, R. A. Zakour,Methods Enzymol. 154, 367-382] with the oligonucleotides 5′-GCC TTT GACAGG TAC CAG GAG TTT G-3′ (SEQ ID NO:18) and 5′-CCA ACT ATA CCA CTC TCGAGG TCT ATT CGA TM C-3′ (SEQ ID NO:19), respectively. The later oligoalso introduced a+1 frameshift (italicized) to terminate translationfrom the starting vector and minimize wild-type background in thephagemid library. This strating vector was designated pH0508B. The helix1 library, which mutated hGH residues 10, 14, 18, 21, was constructed byligating to the large XhoI-KpnI fragment of pH0508B a cassette made fromthe complementary oligonucleotides 5′-pTCG AGG CTC NNS GAC AAC GCG NNSCTG CGT GCT NNS CGT CTT NNS CAG CTG GCC TTT GAC ACG TAC-3′ (SEQ IDNO:20) and 5′-pGT GTC MA GGC CAG CTG SNN MG ACG SNN AGC ACG CAG SNN CGCGTT GTC SNN GAG CC-3′ (SEQ ID NO:21). The KpnI site was destroyed in thejunction of the ligation product so that restriction enzyme digestioncould be used for analysis of non-mutated background.

The library contained at least 10⁷ independent transformants so that ifthe library were absolutely random (10⁶ different combinations ofcodons) we would have an average of about 10 copies of each possiblemutated hGH gene. Restriction analysis using KpnI indicated that atleast 80% of helix 1 library constructs contained the inserted cassette.

Binding enrichments of hGH-phage from the libraries was carried outusing hGHbp immobilized on oxirane-polyacrylamide beads (Sigma ChemicalCo.) as described (Example VIII). Four residues in helix 1 (F10, M14,H18, and H21) were similarly mutated and after 4 and 6 cycles anon-wild-type consensus developed (Table VIII). Position 10 on thehydrophobic face of helix 1 tended to be hydrophobic whereas positions21 and 18 on the hydrophillic face tended were dominated by Asn; noobvious consensus was evident for position 14 (Table IX).

The binding constants for these mutants of hGH to hGHbp was determinedby expressing the free hormone variants in the non-suppressor E. colistrain 16C9, purifying the protein, and assaying by competitivedisplacement of labelled wt-hGH from hGHbp (see Example VIII). Asindicated, several mutants bind tighter to hGHbp than does wt-hGH. TABLEVIII Selection of hGH helix 1 mutants Variants of hGH (randomly mutatedat residues F10, M14, H18, H21) expressed on phagemid particles wereselected by binding to hGHbp-beads and eluting with hGH (0.4 mM) bufferfollowed by glycine (0.2 M, pH 2) buffer (see Example VIII). Gly elutionF10 M14 H18 H21 4 Cycles H G N N A W D N (2) Y T V N I N I N L N S H F SF G 6 Cycles H G N N (6) F S F L Consensus: H G N N

TABLE IX Consensus sequences from the selected helix 1 library Observedfrequency is fraction of all clones sequenced with the indicated aminoacid. The nominal frequency is calculated on the basis of NNS 32 codondegeneracy. The maximal enrichment factor varies from 11 to 32 dependingupon the nominal frequency value for a given residue. Values of[K_(d)(Ala mut)/K_(d)(wt hGH)] for single alanine mutations were takenfrom B. C. Cunningham and J. A. Wells, Science 244, 1081 (1989); B.C.Cunningham, D. J. Henner, J. A. Wells, Science 247, 1461 (1990); B. C.Cunningham and J. A. Wells, Proc. Natl. Acad. Sci. USA 88, 3407 (1991).Wild type residue$\frac{K_{d}\left( {{Ala}\quad{mut}} \right)}{K_{d}\left( {{wt}\quad{hGH}} \right)}$Selected residue    Frequency observed nominal Enrichment F10 5.9 H 0.50   0.031 17 F  0.14   0.031 5 A  0.14   0.062 2 M14 2.2 G 0.50   0.062 8 W  0.14   0.031 5 N  0.14   0.031 5 S  0.14   0.093 2H18 1.6 N  0.50   0.031 17 D  0.14   0.031 5 F  0.14   0.031 5 H21 0.33N  0.79   0.031 26 H  0.07   0.031 2

TABLE X Binding of purified hGH helix 1 mutants to hGHbp Competitionbinding experiments were performed using [¹²⁵I]hGH (wild-type), hGHbp(containing the extracellular receptor domain, residues 1-238), andMab263 [B. C. Cunningham, P. Jhurani, P. Ng, J. A. Wells, Science 243,1330 (1989)];. The number P indicates the fractional occurrence of eachmutant among all the clones sequenced after one or more rounds ofselection. Sequence position 10 14 18 21 P K_(d) (nM)\f(K_(d) mut)K_(d)(wt hGH)) H G N N 0.50 0.14 ± 0.04  0.42 A W D N 0.14 0.10 ± 0.03 0.30 wt = F M H H 0 0.34 ± 0.05 (1)   F S F L 0.07 0.68 ± 0.19 2.0 Y TV N 0.07 0.75 ± 0.19 2.2 L N S H 0.07 0.82 ± 0.20 2.4 I N I N 0.07  1.2± 0.31 3.4

Example X Selection of hGH Variants from a Helix-4 Random CassetteLibrary Containing Previously Found Mutations by Enrichment ofHormone-Phage

Design of Mutant Proteins with Improved Binding Properties by IterativeSelection Using Hormone-Phage

Our experience with recruiting non-binding homologs of hGH evolutionaryvariants suggests that many individual amino acid substitutions can becombined to yield cumulatively improved mutants of hGH with respect tobinding a particular receptor [B. C. Cunningham, D. J. Henner, J. A.Wells, Science 247, 1461 (1990); B. C. Cunningham and J. A. Wells, Proc.Natl. Acad. Sci. USA 88, 3407 (1991); H. B. Lowman, B. C. Cunningham, J.A. Wells, J. Biol. Chem. 266, in press (1991)].

The helix 4b library was constructed in an attempt to further improvethe helix 4 double mutant (E174S/F176Y) selected from the helix 4alibrary that we found bound tighter to the hGH receptor (see ExampleVIII). With the E174S/F176Y hGH mutant as the background startinghormone, residues were mutated that surrounded positions 174 and 176 onthe hydrophilic face of helix 4 (R167, D171, T175 and I179).

Construction of the Helix 4b Library by Cassette Mutagenesis

Cassette mutagenesis was carried out essentially as described [J. A.Wells, M. Vasser, D. B. Powers, Gene 34, 315 (1985)]. The helix 4blibrary, which mutated residues 167, 171, 175 and 179 within theE174S/F176Y background, was constructed using cassette mutagenesis thatfully mutated four residues at a time (see Example VIII) and whichutilized a mutated version of phGHam-g3 into which unique BstEII andBg/II restriction sites had been inserted previously (Example VIII).Into the BstEII-Bg/II sites of the vector was inserted a cassette madefrom the complementary oligonucleotides 5′-pG TTA CTC TAC TGC TTC NNSAAG GAC ATG NNS AAG GTC AGC NNS TAC CTG CGC NNS GTG CAG TGC A-3′ (SEQ IDNO:22) and 5′-pGA TCT GCA CTG CAC SNN GCG CAG GTA SNN GCT GAC CTT SNNCAT GTC CTT SNN GM GCA GTA GA-3′ (SEQ ID NO:23). The BstEII site waseliminated in the ligated cassette. From the helix 4b library, 15unselected clones were sequenced. Of these, none lacked a cassetteinsert, 20% were frame-shifted, and 7% had a non-silent mutation.

Results of hGHbp Enrichment

Binding enrichments of hGH-phage from the libraries was carried outusing hGHbp immobilized on oxirane-polyacrylamide beads (Sigma ChemicalCo.) as described (Example VIII). After 6 cycles of binding a reasonablyclear consensus developed (Table XI). Interestingly, all positionstended to contain polar residues, notably Ser, Thr and Asn (XII).

Assay of hGH Mutants

The binding constants for some of these mutants of hGH to hGHbp wasdetermined by expressing the free hormone variants in the non-suppressorE. coli strain 16C9, purifying the protein, and assaying by competitivedisplacement of labelled wt-hGH from hGHbp (see Example VIII). Asindicated, the binding affinities of several helix-4b mutants for hGHbpwere tighter than that of wt-hGH Table XIII).

Receptor-Selectivity of hGH Variants

Finally, we have begun to analyze the binding affinity of several of thetighter hGHbp binding mutants for their ability to bind to the hPRLbp.The E174S/F176Y mutant binds 200-fold weaker to the hPRLbp than hGH. TheE174T/F176Y/R178K and R167N/D171S/E174S/F176Y/I179T mutants eachbind >500-fold weaker to the hPRLbp than hGH. Thus, it is possible touse the produce new receptor selective mutants of hGH by phage displaytechnology.

Hormone-Phagemid Selection Identifies the Information-Content ofParticular Residues

Of the 12 residues mutated in three hGH-phagemid libraries (ExamplesVIII, IX, X), 4 showed a strong, although not exclusive, conservation ofthe wild-type residues (K172, T175, F176, and R178). Not surprisingly,these were residues that when converted to Ala caused the largestdisruptions (4- to 60-fold) in binding affinity to the hGHbp. There wasa class of 4 other residues (F10, M14, D171, and I179) where Alasubstitutions caused weaker effects on binding (2- to 7-fold) and thesepositions exhibited little wild-type consensus. Finally the other 4residues (H18, H21, R167, and E174), that promote binding to he hPRLbpbut not the hGHbp, did not exhibit any consensus for the wild-type hGHsequence by selection on hGHbp-beads. In fact two residues (E174 andH21), where Ala substitutions enhance binding affinity to the hGHbp by2- to 4-fold [B. C. Cunningham, P. Jhurani, P. Ng, J. A. Wells, Science243, 1330 (1989); B. C. Cunningham and J. A. Wells, Science 244, 1081(1989); B. C. Cunningham, D. J. Henner, J. A. Wells, Science 247, 1461(1990); B. C. Cunningham and J. A. Wells, Proc. Natl. Acad. Sci. USA 88,3407 (1991)]. Thus, the alanine-scanning mutagenesis data correlatesreasonably well with the flexibility to substitute each position. Infact, the reduction in binding affinity caused by alanine substitutions[B. C. Cunningham, P. Jhurani, P. Ng, J. A. Wells, Science 243, 1330(1989); B. C. Cunningham and J. A. Wells, Science 244, 1081 (1989)], B.C. Cunningham, D. J. Henner, J. A. Wells, Science 247, 1461 (1990); B.C. Cunningham and J. A. Wells, Proc. Natl. Acad. Sci. USA 88, 3407(1991)] is a reasonable predictor of the percentage that the wild-typeresidue is found in the phagemid pool after 3-6 rounds of selection. Thealanine-scanning information is useful for targeting side-chains thatmodulate binding, and the phage selection is appropriate for optimizingthem and defining the flexibility of each site (and/or combinations ofsites) for substitution. The combination of scanning mutational methods[B. C. Cunningham, P. Jhurani, P. Ng, J. A. Wells, Science 243, 1330(1989); B. C. Cunningham and J. A. Wells, Science 244, 1081 (1989)] andphage display is a powerful approach to designing receptor-ligandinterfaces and studying molecular evolution in vitro.

Variations on Iterative Enrichment of Hormone-Phagemid Libraries

In cases where combined mutations in hGH have additive effects onbinding affinity to receptor, mutations learned through hormone-phagemidenrichment to improve binding can be combined by simple cutting andligation of restriction fragments or mutagenesis to yield cumulativelyoptimized mutants of hGH.

On the other hand, mutations in one region of hGH which optimizereceptor binding may be structurally or functionally incompatible withmutations in an overlapping or another region of the molecule in thesecases, hormone phagemid enrichment can be carried out by one of severalvariations on the iterative enrichment approach: (1) random DNAlibraries can be generated in each of two (or perhaps more) regions ofthe molecule by cassette or another mutagenesis method. Thereafter, acombined library can be created by ligation of restriction fragmentsfrom the two DNA libraries; (2) an hGH variant, optimized for binding bymutation in one region of the molecule, can be randomly mutated in asecond region of the molecule as in the helix-4b library example; (3)two or more random libraries can be partially selected for improvedbinding by hormone-phagemid enrichment; after this “roughing-in” of theoptimized binding site, the still-partially-diverse libraries can berecombined by ligation of restriction fragments to generate a singlelibrary, partially diverse in two or more regions of the molecules,which in turn can be further selected for optimized binding usinghormone-phagemid enrichment. TABLE XI Mutant phagemids of hGH selectedfrom helix 4b library after 4 and 6 cycles of enrichment. Selection ofhGH helix 4b mutants (randomly mutated at residues 167, 171, 175, 179),each containing the E174S/F176Y double mutant, by binding to hGHbp-beadsand eluting with hGH (0.4 mM) buffer followed by glycine (0.2 M, pH 2)buffer. One mutant (+) contained the spurious mutation R178H. R167 D171T175 I179 4 Cycles N S T T K S T T S N T T D S T T D S T T+ D S A T D SA N T D T T N D T N A N T N A S T T 6 Cycles N S T T (2) N N T T N S T QD S S T E S T I K S T L Consensus: N S T T D N

TABLE XII Consensus sequences from the selected library Observedfrequency is fraction of all clones sequenced with the indicated aminoacid. The nominal frequency is calculated on the basis of NNS 32 codondegeneracy. The maximal enrichment factor varies from 11 to 16 to 32depending upon the nominal frequency value for a given residue. Valuesof [K_(d)(Ala mut)/K_(d)(wt hGH)] for single alanine mutations weretaken from refs. below; for position 175 we only have a value for theT175S mutant [B. C. Cunningham, P. Jhurani, P. Ng, J. A. Wells, Science243, 1330 (1989); B. C. Cunningham and J. A. Wells, Science 244, 1081(1989); B. C. Cunningham, D. J. Henner, J. A. Wells, Science 247, 1461(1990); B. C. Cunningham and J. A. Wells, Proc. Natl. Acad. Sci. USA 88,3407 (1991).]. Wild type residue$\frac{K_{d}\left( {{Ala}\quad{mut}} \right)}{K_{d}\left( {{wt}\quad{hGH}} \right)}$Selected residue    Frequency observed nominal Enrichment R167 0.75 N 0.35   0.031 11 D  0.24   0.031 8 K  0.12   0.031 4 A  0.12   0.062 2D171 7.1 S  0.76   0.093 8 N  0.18   0.031 6 D  0.12   0.031 4 T175 3.5T  0.88   0.062 14 A  0.12   0.031 4 I179 2.7 T  0.71   0.062 11 N 0.18   0.031 6

TABLE XIII Binding of purified hGH mutants to hGHbp. Competition bindingexperiments were performed using [¹²⁵I]hGH (wild-type), hGHbp(containing the extracellular receptor domain, residues 1-238), andMab263 (11). The number P indicates the fractional occurrence of eachmutant among all the clones sequenced after one or more rounds ofselection. Note that the helix 4b mutations (*) are in the background ofhGH(E174S/F176Y). In the list of helix 4b mutants, the E174S/F176Ymutant (*), with wt residues at 167, 171, 175, 179, is shown in bold.Sequence position * * * * K _(d) (Ala mut) 167 171 175 179 P K_(d) (nM)K_(d)(wt hGH) N S T T 0.18 0.04 ± 0.02 0.12 E S T I 0.06 0.04 ± 0.020.12 K S T L 0.06 0.05 ± 0.03 0.16 N N T T 0.06 0.06 ± 0.03 0.17 R D T I0 0.06 ± 0.01 (0.18) N S T Q 0.06 0.26 ± 0.11 0.77

Example XI Assembly of F_(ab) Molecule on the Phagemid Surface

Construction of Plasmids

Plasmid pDH 188 contains the DNA encoding the F_(ab) portion of ahumanized IgG antibody, called 4D5, that recognizes the HER-2 receptor.This plasmid is contained in E. coli strain SR 101, and has beendeposited with the ATCC in Rockville, Md.

Briefly, the plasmid was prepared as follows: the starting plasmid waspS0132, containing the alkaline phosphatase promoter as described above.The DNA encoding human growth hormone was excised and, after a series ofmanipulations to make the ends of the plasmid compatible for ligation,the DNA encoding 4D5 was inserted. The 4D5 DNA contains two genes. Thefirst gene encodes the variable and constant regions of the light chain,and contains at its 5′ end the DNA encoding the st II signal sequence.The second gene contains four portions: first, at its 5′ end is the DNAencoding the st II signal sequence. This is followed by the DNA encodingthe variable domain of the heavy chain, which is followed by the DNAencoding the first domain of the heavy chain constant region, which inturn is followed by the DNA encoding the M13 gene III. The salientfeatures of this construct are shown in FIG. 10. The sequence of the DNAencoding 4D5 is shown in FIG. 11.

E. coli Transformation and Phage Production.

Both polyethylene glycol (PEG) and electroporation were used totransform plasmids into SR101 cells. (PEG competent cells were preparedand transformed according to the method of Chung and Miller (NucleicAcids Res. 16:3580 [1988]). Cells that were competent forelectroporation were prepared, and subsequently transformed viaelectroporation according to the method of Zabarovsky and Winberg(Nucleic Acids Res. 18:5912 [1990]). After placing the cells in 1 ml ofthe SOC media (described in Sambrook et al, supra), they were grown for1 hour at 37° C. with shaking. At this time, the concentration of thecells was determined using light scattering at OD₆₀₀. A titered KO7phage stock was added to achieve an multiplicity of infection (MOI) of100, and the phage were allowed to adhere to the cells for 20 minutes atroom temperature. This mixture was then diluted into 25 mis of 2YT broth(described in Sambrook et al., supra) and incubated with shaking at 37°C. overnight. The next day, cells were pelleted by centrifugation at5000×g for 10 minutes, the supernatant was collected, and the phageparticles were precipitated with 0.5 M NaCl and 4% PEG (finalconcentration) at room temperature for 10 minutes. Phage particles werepelleted by centrifugation at 10,000×g for 10 minutes, resuspended in 1ml of TEN (10 mM Tris, pH 7.6, 1 mM EDTA, and 150 mM NaCl), and storedat 4° C.

Production of Antigen Coated Plates.

Aliquots of 0.5 ml from a solution of 0.1 mg/ml of the extra-cellulardomain of the HER-2 antigen (ECD) or a solution of 0.5 mg/ml of BSA(control antigen) in 0.1 M sodium bicarbonate, pH 8.5 were used to coatone well of a Falcon 12 well tissue culture plate. Once the solution wasapplied to the wells, the plates were incubated at 4° C. on a rockingplatform overnight. The plates were then blocked by removing the initialsolution, applying 0.5 ml of blocking buffer (30 mg/ml BSA in 0.1 Msodium bicarbonate), and incubating at room temperature for one hour.Finally, the blocking buffer was removed, 1 ml of buffer A (PBS, 0.5%BSA, and 0.05% Tween-20) was added, and the plates were stored up to 10days at 4° C. before being used for phage selection.

Phage Selection Process.

Approximately 10⁹ phage particles were mixed with a 100-fold excess ofKO7 helper phage and 1 ml of buffer A. This mixture was divided into two0.5 ml aliquots; one of which was applied to ECD coated wells, and theother was applied to BSA coated wells. The plates were incubated at roomtemperature while shaking for one to three hours, and were then washedthree times over a period of 30 minutes with 1 ml aliquots of buffer A.Elution of the phage from the plates was done at room temperature by oneof two methods: 1) an initial overnight incubation of 0.025 mg/mlpurified Mu4D5 antibody (murine) followed by a 30 minute incubation with0.4 ml of the acid elution buffer (0.2 M glycine, pH 2.1, 0.5% BSA, and0.05% Tween-20), or 2) an incubation with the acid elution buffer alone.Eluates were then neutralized with 1 M Tris base, and a 0.5 ml aliquotof TEN was added. These samples were then propagated, titered, andstored at 4° C.

Phage Propagation

Aliquots-of eluted phage were added to 0.4 ml of 2YT broth and mixedwith approximately 10⁸ mid-log phase male E. coli strain SR101. Phagewere allowed to adhere to the cells for 20 minutes at room temperatureand then added to 5 ml of 2YT broth that contained 50 μg/ml ofcarbenicillin and 5 μg/ml of tetracycline. These cells were grown at 37°C. for 4 to 8 hours until they reached mid-log phase. The OD₆₀₀ wasdetermined, and the cells were superinfected with KO7 helper phage forphage production. Once phage particles were obtained, they were titeredin order to determine the number of colony forming units (cfu). This wasdone by taking aliquots of serial dilutions of a given phage stock,allowing them to infect mid-log phase SR101, and plating on LB platescontaining 50 μg/ml carbenicillin.

RIA Affinity Determination.

The affinity of h4D5 F_(ab) fragments and F_(ab) phage for the ECDantigen was determined using a competitive receptor binding RIA (Burt,D. R., Receptor Binding in Drug Research. O'Brien, R. A. (Ed.). pp.3-29, Dekker, New York [1986]). The ECD antigen was labeled with¹²⁵-Iodine using the sequential chloramine-T method (De Larco, J. E. etal., J. Cell. Physiol. 109:143-152 [1981 ]) which produced a radioactivetracer with a specific activity of 14 μCi/μg and incorporation of 0.47moles of Iodine per mole of receptor. A series of 0.2 ml solutionscontaining 0.5 ng (by ELISA) of F_(ab) or F_(ab) phage, 50 nCi of ¹²⁵IECD tracer, and a range of unlabeled ECD amounts (6.4 ng to 3277 ng)were prepared and incubated at room temperature overnight. The labeledECD-F_(ab) or ECD-F_(ab) phage complex was separated from the unboundlabeled antigen by forming an aggregate complex induced by the additionof an anti-human IgG (Fitzgerald 40-GH23) and 6% PEG 8000. The complexwas pelleted by centrifugation (15,000×g for 20 minutes) and the amountof labeled ECD (in cpm) was determined by a gamma counter. Thedissociation constant (K_(d)) was calculated by employing a modifiedversion of the program LIGAND (Munson, P. and Rothbard, D., Anal.Biochem. 107:220-239 [1980]) which utilizes Scatchard analysis(Scatchard, G., Ann. N.Y. Acad. Sci. 51:660-672 [1949]). The Kd valuesare shown in FIG. 13.

Competitive Cell Binding Assay

Murine 4D5 antibody was labeled with 125-I to a specific activity of40-50 μCi/μg using the lodogen procedure. Solutions containing aconstant amount of labeled antibody and increasing amounts of unlabeledvariant Fab were prepared and added to near confluent cultures ofSK-BR-3 cells grown in 96-well microtiter dishes (final concentration oflabeled antibody was 0.1 nM). After an overnight incubation at 4° C.,the supernatant was removed, the cells were washed and the cellassociated radioactivity was determined in a gamma counter. K_(d) valueswere determined by analyzing the data using a modified version of theprogram LIGAND (Munson, P. and Rothbard, D., supra)

This deposit of plasmid pDH188 ATCC no. 68663 was made under theprovisions of the Budapest Treaty on the International Recognition ofthe Deposit of Microorganisms for the Purpose of Patent Procedure andthe Regulations thereunder (Budapest Treaty). This assures maintenanceof a viable culture for 30 years from the date of deposit. The organismswill be made available by ATCC under the terms of the Budapest Treaty,and subject to an agreement between Genentech, Inc. and ATCC, whichassures permanent and unrestricted availability of the progeny of thecultures to the public upon issuance of the pertinent U.S. patent orupon laying open to the public of any U.S. or foreign patentapplication, whichever comes first, and assures availability of theprogeny to one determined by the U.S. Commissioner of Patents andTrademarks to be entitled thereto according to 35 USC §122 and theCommissioner's rules pursuant thereto (including 37 CFR §1.14 withparticular reference to 886 OG 638).

The assignee of the present application has agreed that if the cultureson deposit should die or be lost or destroyed when cultivated undersuitable conditions, they will be promptly replaced on notification witha viable specimen of the same culture. Availability of the depositedcultures is not to be construed as a license to practice the inventionin contravention of the rights granted under the authority of anygovernment in accordance with its patent laws.

The foregoing written specification is considered to be sufficient toenable one skilled in the art to practice the invention. The presentinvention is not to be limited in scope by the cultures deposited, sincethe deposited embodiments are intended as separate illustrations ofcertain aspects of the invention and any cultures that are functionallyequivalent are within the scope of this invention. The deposit ofmaterial herein does not constitute an admission that the writtendescription herein contained is inadequate to enable the practice of anyaspect of the invention, including the best mode thereof, nor is it tobe construed as limiting the scope of the claims to the specificillustrations that it represents. Indeed, various modifications of theinvention in addition to those shown and described herein will becomeapparent to those skilled in the art from the foregoing description andfall within the scope of the appended claims.

While the invention has necessarily been described in conjunction withpreferred embodiments, one of ordinary skill, after reading theforegoing specification, will be able to effect various changes,substitutions of equivalents, and alterations to the subject matter setforth herein, without departing from the spirit and scope thereof.Hence, the invention can be practiced in ways other than thosespecifically described herein. It is therefore intended that theprotection granted by Letters Patent hereon be limited only by theappended claims and equivalents thereof.

Example XII Selection of hGH Variants from Combinations of Helix-1 andHelix-4 Hormone-Phage Variants

Construction of Additive Variants of hGH

According to additivity principles [J. A. Wells, Biochemistry 29, 8509(1990)], mutations in different parts of a protein, if they are notmutually interacting, are expected to combine to produce additivechanges in the free energy of binding to another molecule (changes areadditive in terms of ΔΔG_(binding), or multiplicative in terms ofK_(d)=exp[−ΔG/RT]). Thus a mutation producing a 2-fold increase inbinding affinity, when combined with a second mutation causing a 3-foldincrease, would be predicted to yield a double mutant with a 6-foldincreased affinity over the starting variant.

To test whether multiple mutations obtained from hGH-phage selectionswould produce cumulatively favorable effects on hGHbp (hGH-bindingprotein; the extracellular domain of the hGH receptor) binding, wecombined mutations found in the three tightest-binding variants of hGHfrom the helix-1 library (Example IX: F10A/M14W/H18D/H21N,F10H/M14G/H18N/H21N, and F10F/M14S/H18F/H21L) with those found in thethree tightest binding variants found in the helix-4b library (ExampleX: R167N/D171S/T175/1179T, R167E/D171S/T175/I179; andR167N/D171N/T175/I179T).

hGH-phagemid double~stranded DNA (dsDNA) from each of the one-helixvariants was isolated and digested with the restriction enzymes EcoRIand BstXI. The large fragment from each helix-4b variant was thenisolated and ligated with the small fragment from each helix-1 variantto yield the new two-helix variants shown in Table XIII. All of thesevariants also contained the mutations E174S/F176Y obtained in earlierhGH-phage binding selections (see Example X for details).

Construction of Selective Combinatorial Libraries of hGH

Although additivity principles appear to hold for a number ofcombinations of mutations, some combinations (e.g. E174S with F176Y) areclearly non-additive (see examples VIII and X). In order to identifywith certainty the tightest binding variant with, for example, 4mutations in helix-1 and 4 mutations in helix-4, one would ideallymutate all 8 residues at once and then sort the pool for the globallytightest binding variant. However, such a pool would consist of 1.1×10¹²DNA sequences (utilizing NNS codon degeneracy) encoding 2.6×10¹⁰different polypeptides. Obtaining a random phagemid library large enoughto assure representation of all variants (perhaps 10¹³ transformants) isnot practical using current transformation technology.

We have addressed this difficulty first by utilizing successive roundsof mutagenesis, taking the tightest binding variant from one library,then mutating other residues to further improve binding (Example X). Ina second method, we have utilized the principle of additivity to combinethe best mutations from two independently sorted libraries to createmultiple mutants with improved binding (described above). Here, wefurther searched through the possible combinations of mutations atpositions 10, 14, 18, 21, 167, 171, 175, and 179 in hGH, by creatingcombinatorial libraries of random or partially-random mutants. Weconstructed three different combinatorial libraries of hGH-phagemids,using the pooled phagemids from the helix 1 library.(independentlysorted for 0, 2, or 4 cycles; Example IX) and the pool from the helix-4blibrary (independently sorted for 0, 2, or 4 cycles; Example X) andsorted the combined variant pool for hGHbp binding. Since some amount ofsequence diversity exists in each of these pools, the resultingcombinatorial library can explore more sequence combinations than whatwe might construct manually (e.g. Table XIII).

hGH-phagemid double-stranded DNA (dsDNA) from each of the one-helixlibrary pools (selected for 0, 2, or 4 rounds) was isolated and digestedwith the restriction enzymes AccI and BstXI. The large fragment fromeach helix-1 variant pool was then isolated and ligated with the smallfragment from each helix-4b variant pool to yield the threecombinatorial libraries pH0707A (unselected helix 1 and helix 4b pools,as described in examples IX and X), pH0707B (twice-selected helix-1 poolwith twice-selected helix-4b pool), and pH0707C (4-times selectedhelix-1 pool with 4-times selected helix-4b pool). Duplicate ligationswere also set up with less DNA and designated as pH0707D, ph0707E, andph0707F, corresponding to the 0-,2-, and 4-round starting librariesrespectively. All of these variant pools also contained the mutationsE174S/F176Y obtained in earlier hGH-phage binding selections (seeExample X for details).

Sorting Combinatorial Libraries of hGH-Phage Variants

The ligation products ph0707A-F were processed and electro-transformedinto XL1-Blue cells as described (Example VIII). Based on colony-formingunits (CFU), the number of transformants obtained from each pool was asfollows: 2.4×10⁶ from ph0707A, 1.8×10⁶ from ph0707B, 1.6×10⁶ fromph0707C, 8×10⁵ from ph0707D, 3×10⁵ from ph0707E, and 4×10⁵ from ph0707F.hGH-phagemidparticles were prepared and selected for hGHbp-binding over2 to 7 cycles as described in Example VIII.

Rapid Sorting of hGH-Phagemid Libraries

In addition to sorting phagemid libraries for tight-binding proteinvariants, as measured by equilibrium binding affinity, it is of interestto sort for variants which are altered in either the on-rate (k_(on)) orthe off-rate (k_(off)) of binding to a receptor or other molecule. Fromthermodynamics, these rates are related to the equilibrium dissociationconstant, K_(d)=(k_(off)/k_(on)) We envision that certain variants of aparticular protein have similar K_(d)'s for binding while having verydifferent k_(on)'s and k_(off)'s. Conversely, changes in K_(d) from onevariant to another may be due to effects on k_(on), effects on k_(off),or both. The pharmacological properties of a protein may be dependent onbinding affinity or on k_(on) or k_(off), depending on the detailedmechanism of action. Here, we sought to identify hGH variants withhigher on-rates to investigate the effects of changes in k_(on). Weenvision that the selection could alternatively be weighted towardk_(off) by increasing the binding time and increasing the wash timeand/or concentration with cognate ligand (hGH).

From time-course analysis of wild-type hGH-phagemid binding toimmobilized hGHbp, it appears that, of the total hGH-phagemid particlesthat can be eluted in the final pH 2 wash (see Example VIII for thecomplete binding and elution protocol), less than 10% are bound after 1minute of incubation, while greater than 90% are bound after 15 minutesof incubation.

For “rapid-binding selection,” phagemid particles from the ph0707B pool(twice-selected for helices 1 and 4 independently) were incubated withimmobilized hGHbp for only 1 minute, then washed six times with 1 mL ofbinding buffer; the hGH-wash step was omitted; and the remaininghGH-phagemid particles were eluted with a pH2 (0.2M glycine in bindingbuffer) wash. Enrichment of hGH-phagemid particles over non-displayingparticles indicated that even with a short binding period and nocognate-ligand (hGH) challenge, hGH-phagemid binding selection sortstight-binding variants out of a randomized pool.

Assay of hGH Mutants

The binding constants for some of these mutants of hGH to hGHbp wasdetermined by expressing the free hormone variants in the non-suppressorE. coli strain 16C9 or 34B8, purifying the protein, and assaying bycompetitive displacement of labelled wt-hGH from hGHbp (see ExampleVIII) in a radio-immunoprecipitation assay. In Table XIII below, all thevariants have glutamate₁₇₄ replaced by serine₁₇₄ and phenylalanine₁₇₆replaced by tyrosine₁₇₆ (E174S and F1176Y) plus the additionalsubstitutions as indicated at hGH amino acid positions 10, 14, 18, 21,167, 171, 175 and 179. TABLE XIII-A hGH variants from addition ofhelix-1 and helix-4b mutations wild-type residue: Helix 1 Helix 4Variant F10 M14 H18 H21 R167 D171 T175 I179 H0650AD H G N N N S T TH0650AE H G N N E S T I H0650AF H G N N N N T T H0650BD A W D N N S T TH0650BE A W D N E S T I H0650BF A W D N N N T T H0650CD F S F L N S T TH0650CD F S F L E S T I H0650CD F S F L N N T T

In Table XIV below, hGH variants were selected from combinatoriallibraries by the phagemid binding selection process. All hGH variants inTable XIV contain two background mutations (E174S/F176Y). hGH-phagemidpools from the libraries ph0707A (Part A), ph0707B and ph0707E (Part B),or ph0707C (Part C) were sorted for 2 to 7 cycles for binding to hGHbp.The number P indicates the fractional occurrence of each variant typeamong the set of clones sequenced from each pool. TABLE XIV hGH variantsfrom hormone-phagemid binding selection of combinatorial libraries.wild-type residue: Helix 1 Helix 4 P Variant F10 M14 H18 H21 R167 D171T175 I179 Part A: 4 cycles: 0.60 H0714A.1 H G N N N S T N 0.40 H0714A.4A N D A N N T N* Part B: 2 cycles: 0.13 H0712B.1 F S F G H S T T 0.13H0712B.2 H Q T S A D N S 0.13 H0712B.4 H G N N N A T T 0.13 H0712B.5 F SF L S D T T 0.13 H0712B.6 A S T N R D T I 0.13 H0712B.7 Q Y N N H S T T0.13 H0712B.8 W G S S R D T I 0.13 H0712E.1 F L S S K N T V 0.13H0712E.2 W N N S H S T T 0.13 H0712E.3 A N A S N S T T 0.13 H0712E.4 P SD N R D T I 0.13 H0712E.5 H G N N N N T S 0.13 H0712E.6 F S T G R D T I0.13 H0712E.7 M T S N Q S T T 0.13 H0712E.8 F S F L T S T S 4 cycles:0.17 H0714B.1 A W D N R D T I 0.17 H0714B.2 A W D N H S T N 0.17H0714B.3 M Q M N N S T T 0.17 H0714B.4 H Y D H R D T T 0.17 H0714B.5 L NS H R D T I 0.17 H0714B.6 L N S H T S T T 7 cycles: 0.57 H0717B.1 A W DN N A T T 0.14 H0717B.2 F S T G R D T I 0.14 H0717B.6 A W D N R D T I0.14 H0717B.7 I Q E H N S T T 0.50 H0717E.1 F S L A N S T V Part C: 4cycles: 0.67 H0714C.2 F S F L K D T T*= also contained the mutations L15R, K168R.

In Table XV below, hGH variants were selected from combinatoriallibraries by the phagemid binding selection process. All hGH variants inTable XV contain two background mutations (E174S/F176Y). The number P isthe fractional occurrence of a given variant among all clones sequencedafter 4 cycles of rapid-binding selection. TABLE XV hGH variants fromRAPID hGHbp binding selection of an hGH-phagemid combinatorial librarywild-type residue: Helix 1 Helix 4 P Variant F10 M14 H18 H21 R167 D171T175 I179 0.14 H07BF4.2 W G S S R D T I 0.57 H07BF4.3 M A D N N S T T0.14 H07BF4.6 A W D N S S V T‡ 0.14 H07BF4.7 H Q T S R D T I‡= also contained the mutation Y176F (wild-type hGH also contains F176).

In table XVI below, binding constants were measured by competitivedisplacement of ¹²⁵I-labelled hormone H0650BD or labelled hGH usinghGHbp (1-238) and either Mab5 or Mab263. The variant H0650BD appearsbind more than 30-fold tighter than wild-type hGH. TABLE XVI Equilibriumbinding constants of selected hGH variants. hGH Kd(variant) Kd(variant)Variant {overscore (Kd(H0650BD))} Kd(hGH) Kd (pM) hGH 32 -1- 340 ± 50 H0650BD -1- 0.031 10 ± 3  H0650BF 1.5 0.045 15 ± 5  H0714B.6 3.4 0.09934 ± 19 H0712B.7 7.4 0.22 74 ± 30 H0712E.2 16 0.48 60 ± 70

Example XIII Selective Enrichment of hGH-Phage Containing a ProteaseSubstrate Sequence Versus Non-Substrate Phage

As described in Example I, the plasmid pS0132 contains the gene for hGHfused to the residue Pro198 of the gene III protein with the insertionof an extra glycine residue. This plasmid may be used to producehGH-phage particles in which the hGH-gene III fusion product isdisplayed monovalently on the phage surface (Example IV). The fusionprotein comprises the entire hGH protein fused to the carboxy terminaldomain of gene III via a flexible linker sequence.

To investigate the feasibility of using phage display technology toselect favourable substrate sequences for a given proteolytic enzyme, agenetically engineered variant of subtilisin BPN′ was used. (Carter, P.et al., Proteins: Structure, function and genetics 6:240-248 (1989)).This variant (hereafter referred to as A64SAL subtilisin) contains thefollowing mutations: Ser24Cys, His64Ala, Glu156Ser, Gly169Ala andTyr217Leu. Since this enzyme lacks the essential catalytic residueHis64, its substrate specificity is greatly restricted so that certainhistidine-containing substrates are preferentially hyrdrolysed (Carteret al., Science 237:394-399 (1987)).

Construction of a hGH-Substrate-Phage Vector

The sequence of the linker region in pS0132 was mutated to create asubstrate sequence for A64SAL subtilisin, using the oligonucleotide5′-TTC-GGG-CCC-TTC-GCT-GCT-CAC-TAT-ACG-CGT-CAG-TCG-ACT-GAC-CTG-CCT-3′(SEQ ID NO:27). This resulted in the introduction of the proteinsequence Phe-Gly-Pro-Phe-Ala-Ala-His-Tyr-Thr-Arg-Gln-Ser-Thr-Asp (SEQ IDNO:107) in the linker region between hGH and the carboxy terminal domainof gene III, where the first Phe residue in the above sequence is Phe191of hGH. The sequence Ala-Ala-His-Tyr-Thr-Agr-Gln (SEQ ID NO:97) is knownto be a good substrate for A64SAL subtilisin (Carter et al (1989),supra). The resulting plasmid was designated pS0640.

Selective Enrichment of hGH-Substrate-Phage

Phagemid particles derived from pS0132 and pS0640 were constructed asdescribed in Example I. In initial experiments, a 10 μl aliquot of eachphage pool was separately mixed with 30 μl of oxirane beads (prepared asdescribed in Example II) in 100 μl of buffer comprising 20 mM Tris-HClpH 8.6 and 2.5M NaCl. The binding and washing steps were performed asdescribed in example VII. The beads were then resuspended in 400 μl ofthe same buffer, with or without 50 nM of A64SAL subtilisin. Followingincubation for 10 minutes, the supernatants were collected and the phagetitres (cfu) measured. Table XVII shows that approximately 10 times moresubstrate-containing phagemid particles (pS0640) were eluted in thepresence of enzyme than in the absence of enzyme, or than in the case ofthe non-substrate phagemids (pS0132) in the presence or absence ofenzyme. Increasing the enzyme, phagemid or bead concentrations did notimprove this ratio.

Improvement of the Selective Enrichment Procedure

In an attempt to decrease the non-specific elution of immobilisedphagemids, a tight-binding variant of hGH was introduced in place of thewild-type hGH gene in pS0132 and pS0640. The hGH variant used was asdescribed in example XI (pH0650bd) and contains the mutations Phe10Ala,Met14Trp, His18Asp, His21Asn, Arg167Asn, Asp171 Ser, Glu174Ser,Phe176Tyr and Ile179Thr. This resulted in the construction of two newphagemids: pDM0390 (containing tight-binding hGH and no substratesequence) and pDM0411 (containing tight-binding hGH and the substratesequence Ala-Ala-His-Tyr-Thr-Agr-Gln). The binding washing and elutionprotocol was also changed as follows:

(i) Binding: COSTAR 12-well tissue culture plates were coated for 16hours with 0.5 ml/well 2 ug/ml hGHbp in sodium carbonate buffer pH 10.0.The plates were then incubated with 1 ml/well of blocking buffer(phosphate buffered saline (PBS) containing 0.1% w/v bovine serumalbumen) for 2 hours and washed in an assay buffer containing 10 mMTris-HCl pH 7.5, 1 mM EDTA and 100 mM NaCl. Phagemids were againprepared as described in Example I: the phage pool was diluted 1:4 inthe above assay buffer and 0.5 ml of phage incubated per well for 2hours.

(ii) Washing: The plates were washed thoroughly with PBS+0.05% Tween 20and incubated for 30 minuted with 1 ml of this wash buffer. This washingstep was repeated three times.

(iii) Eution: The plates were incubated for 10 minutes in an elutionbuffer consisting of 20 mM Tris-HCl pH 8.6+100 mM NaCl, then the phagewere eluted with 0.5 ml of the above buffer with or without 500 nM ofA64SAL subtilisin.

Table XVII shows that there was a dramatic increase in the ratio ofspecifically eluted substrate-phagemid particles compared to the methodpreviously described for pS0640 and pS0132. It is likely that this isdue to the fact that the tight-binding hGH mutant has a significantlyslower off-rate for binding to hGH binding protein compared to wild-typehGH. TABLE XVII Specific elution of substrate-phagemids by A64SALsubtilisin Colony forming units (cfu) were estimated by plating out 10μl of 10-fold dilutions of phage on 10 μl spots of XL-1 blue cells, onLB agar plates containing 50 μg/ml carbenicillinl phagemid +50 nM A64SALno enzyme (i) Wild-type hGH gene: binding to hGHbp-oxirane beads pS0640(substrate) 9 × 10⁶ cfu/10 μl 1.5 × 10⁶ cfu/10 μl   pS0132(non-substrate) 6 × 10⁵ cfu/10 μl 3 × 10⁵ cfu/10 μl (ii) pH0650bd mutanthGH gene: binding to hGHbp-coated plates pDM0411 (substrate) 1.7 × 10⁵cfu/10 μl   2 × 10³ cfu/10 μl pDM0390 (non- 2 × 10³ cfu/10 μl 1 × 10³cfu/10 μl substrate)

Example XIV Identification of Preferred Substrates for A64SAL SubtilisinUsing Selective Enrichment of a Library of Substrate Sequences

We sought to employ the selective enrichment procedure described inExample XIII to identify good substrate sequences from a library ofrandom substrate sequences.

Construction of a Vector for Insertion of Randomised Substrate Cassettes

We designed a vector suitable for introduction of randomised substratecassettes. and subsequent expression of a library of substratesequences. The starting point was the vector pS0643, described inExample VIII. Site-directed mutagenesis was carried out using theoligonucleotide5′-AGC-TGT-GGC-TTC-GGG-CCC-GCC-GCC-GCG-TCG-ACT-GGC-GGT-GGC-TCT-3′ (SEQID NO:28), which introduces ApaI (GGGCCC) and SalI (GTCGAC) restrictionsites between hGH and Gene III. This new construct was designatedpDM0253 (The actual sequence of pDM0253 is5′-AGC-TGT-GGC-TTC-GGG-CCC-GCC-CCC-GCG-TCG-ACT-GGC-GGT-GGC-TCT-3′ (SEQID NO:291, where the underlined base substitution is due to a spuriouserror in the mutagenic oligonucleotide). In addition, the tight-bindinghGH variant described in example was introduced by exchanging a fragmentfrom pDM0411 (example XIII) The resulting library vector was designatedpDM0454.

Preparation of the Library Cassette Vector and Insertion of theMutagenic Cassette

To introduce a library cassette, pDM0454 was digested with ApaI followedby SalI, then precipitated with 13% PEG 8000+10 mM MgCl₂, washed twicein 70% ethanol and resuspended This efficiently precipitates the vectorbut leaves the small Apa-Sal fragment in solution (Paithankar, K. R. andPrasad, K. S. N., Nucleic Acids Research 19:1346). The product was runon a 1% agarose gel and the Apal-Sall digested vector excised, purifiedusing a Bandprep kit (Pharmacia) and resuspended for ligation with themutagenic cassette.

The cassette to be inserted contained a DNA sequence similar to that inthe linker region of pS0640 and pDM0411, but with the codons for thehistidine and tyrosine residues in the substrate sequence replaced byrandomised codons. We chose to substitute NNS (N=G/A/T/C; S=G/C) at eachof the randomised positions as described in example VIII. Theoligonucleotides used in the mutagenic cassettes were:5′-C-TTC-GCT-GCT-NNS-NNS-ACC-CGG-CAA-3′ (coding strand) (SEQ ID NO:30)and 5′-T-CGA-TTG-CCG-GGT-SNN-SNN-AGC-AGC-GAA-GGG-CC-3′ (non-codingstrand) (SEQ ID NO:31). This cassette also destroys the SalI site, sothat digestion with SalI may be used to reduce the vector background.The oligonucleotides were not phosphorylated before insertion into theApa-Sal cassette site, as it was feared that subsequent oligomerisationof a small population of the cassettes may lead to spurious results withmultiple cassette inserts. Following annealing and ligation, thereaction products were phenol:chloroform extracted, ethanol precipitatedand resuspended in water. Initially, no digestion with SalI to reducethe background vector was performed. Approximately 200 ng waselectroporated into XL-1 blue cells and a phagemid library was preparedas described in example VIII.

Selection of Highly Cleavable Substrates from the Substrate Library

The selection procedure used was identical to that described for pDM0411and pDM0390 in example XIII. After each round of selection, the elutedphage were propagated by transducing a fresh culture of XL-1 blue cellsand propagating a new phagemid library as described for hGH-phage inexample VIII. The progress of the selection procedure was monitored bymeasuring eluted phage titres and by sequencing individual clones aftereach round of selection.

Table A shows the successive phage titres for elution in the presenceand absence of enzyme after 1, 2 and 3 rounds of selection.

Clearly, the ratio of specifically eluted phage: non-specifically elutedphage (ie phage eluted with enzyme:phage eluted without enzyme)increases dramatically from round 1 to round 3, suggesting that thepopulation of good substrates is increasing with each round ofselection.

Sequencing of 10 isolates from the starting library showed them all toconsist of the wild-type pDM0464 sequence. This is attributed to thefact that after digestion with ApaI, the SalI site is very close to theend of the DNA fragment, thus leading to low efficiency of digestion.Nevertheless, there are only 400 possible sequences in the library, sothis population should still be well represented.

Tables B1 and B2 shows the sequences of isolates obtained after round 2and round 3 of selection. After 2 rounds of selection, there is clearlya high incidence of histidine residues. This is exactly what isexpected: as described in example XIII, A64SAL subtilisin requires ahistidine residue in the substrate as it employs a substrate-assistedcatalytic mechanism. After 3 rounds of selection, each of the 10 clonessequenced has a histidine in the randomised cassette. Note, however,that 2 of the sequences are of pDM0411, which was not present in thestarting library and is therefore a contaminant. TABLE A Titration ofinitial phage pools and eluted phage from 3 rounds of selectiveenrichment Colony forming units (cfu) were estimated by plating out 10μl of 10-fold dilutions of phage on 10 μl spots of XL-1 blue cells, onLB agar plates containing 50 μg/ml carbenicillin ROUND 1 Startinglibrary: 3 × 10¹² cfu/ml LIBRARY: +500 nM A64SAL 4 × 10³ cfu/10 μl noenzyme 3 × 10³ cfu/10 μl pDM0411: +500 nM A64SAL 2 × 10⁶ cfu/10 μl(control) no enzyme 8 × 10³ cfu/10 μl ROUND 2 Round 1 library: 7 × 10¹²cfu/ml LIBRARY: +500 nM A64SAL 3 × 10⁴ cfu/10 μl no enzyme 6 × 10³cfu/10 μl pDM0411: +500 nM A64SAL 3 × 10⁶ cfu/10 μl (control) no enzyme1.6 × 10⁴ cfu/10 μl   ROUND 3 Round 2 library: 7 × 10¹¹ cfu/ml LIBRARY:+500 nM A64SAL 1 × 10⁵ cfu/10 μl no enzyme   <10³ cfu/10 μl pDM0411:+500 nM A64SAL 5 × 10⁶ cfu/10 μl (control) no enzyme 3 × 10⁴ cfu/10 μl

TABLE B1 Sequences of eluted phage after 2 rounds of selectiveenrichment. All protein sequences should be of the form AA**TRQ, where *represents a randomised codon. In the table below, the randomised codonsand amino acids are underlined and in bold. After round 2: No. ofSequence occurrences                *   * 2      A   A   H   Y   T   R   Q (SEQ ID NO:97) ... GCT GCT CAC TAC ACCCGG CAA ... (SEQ ID NO:32)       A   A   H   M   T   R   Q (SEQ IDNO:98) 1 ... GCT GCT CAC ATG ACC CGG CAA ... (SEQ ID NO:33)      A   A   L   H   T   R   Q (SEQ ID NO:99) 1 ... GCT GCT CTC CAC ACCCGG CAA ... (SEQ ID NO:34)       A   A   L   H   T   R   Q (SEQ IDNO:99) 1 ... GCT GCT CTG CAC ACC CGG CAA ... (SEQ ID NO:35)      A   A   H   T   R   Q (SEQ ID NO:100) 1  # ... GCT GCT CAC ACC CGGCAA ... (SEQ ID NO:36)       A   A   ?   H   T   R   Q (SEQ ID NO:101) 1 ## ... GCT GCT ??? CAC ACC CGG CAA (SEQ ID NO:37) ... wild-type pDM04543#- spurious deletion of 1 codon within the cassette##- ambiguous sequence

TABLE B2 Sequences of eluted phage after 3 rounds of selectiveenrichment. All protein sequences should be of the form AA**TRQ, where *represents a randomised codon. In the table below, the randomised codonsand amino acids are underlined and in bold. After round 3: No. ofSequence occurrences                *   * 2#     A   A   H   Y   T   R   Q (SEQ ID NO:97) ... GCT GCT CAC TAT ACGCGT CAG ... (SEQ ID NO:38)       A   A   L   H   T   R   Q (SEQ IDNO:99) 2 ... GCT GCT CTC CAC ACC CGG CAA ... (SEQ ID NO:34)      A   A   Q   H   T   R   Q (SEQ ID NO:102) 1 ... GCT GCTCAG CAC ACC CGG CAA ... (SEQ ID NO:39)       A   A   T   H   T   R   Q(SEQ ID NO:103) 1 ... GCT GCT ACG CAC ACC CGG CAA ... (SEQ ID NO:40)      A   A   H   S   R   Q (SEQ ID NO:104) 1 ... GCT GCT CAC TCC CGGCAA ... (SEQ ID NO:41)       A   A   H   H   T   R   Q (SEQ ID NO:105)1## ... GCT GCT CAT CAT ACC CGG CAA (SEQ ID NO:42)      A   A   H   F   R   Q (SEQ ID NO:106) 1 ... GCT GCT CAC TTC CGGCAA (SEQ ID NO:43)       A   A   H   T   R   Q (SEQ ID NO:100) 1 ... GCTGCT CAC ACC CGG CAA ... (SEQ ID NO:36)#- contaminating sequence from pDM0411##- contains the “illegal” codon CAT - T should not appear in the 3rdposition of a codon.

1. A method for selecting novel binding polypeptides comprising: (a)constructing a replicable expression vector comprising a transcriptionregulatory element operably linked to a gene fusion encoding a fusionprotein wherein the gene fusion comprises a first gene encoding apolypeptide, and a second gene encoding at least a portion of a phagecoat protein; (b) mutating the vector at one or more selected positionswithin the first gene thereby forming a family of related plasmids; (c)transforming suitable host cells with the plasmids; (d) infecting thetransformed host cells with a helper phage having a gene encoding thephage coat protein; (e) culturing the transformed infected host cellsunder conditions suitable for forming recombinant phagemid particlescontaining at least a portion of the plasmid and capable of transformingthe host, the conditions adjusted so that no more than a minor amount ofphagemid particles display more than one copy of the fusion protein onthe surface of the particle; (f) contacting the phagemid particles witha target molecule so that at least a portion of the phagemid particlesbind to the target molecule; and (g) separating the phagemid particlesthat bind from those that do not.
 2. The method of claim 1 furthercomprising infecting a suitable host cells with the phagemid particlesthat bind and repeating steps (d) through (g).
 3. The method of claim 2wherein the steps are repeated one or more times.
 4. The method of claim1 wherein the expression vector further comprises a secretory signalsequence.
 5. The method of claim 1 wherein the transcription regulatoryelement is a promoter system selected from the group; lac Z, pho A,tryptophan, tac, λ_(PL), bacteriophage T7, and combinations thereof. 6.The method of claim 1 wherein the first gene encodes a mammalianprotein.
 7. The method of claim 6 wherein the protein is selected fromthe group; growth hormone, human growth hormone(hGH), des-N-methionylhuman growth hormone, bovine growth hormone, parathyroid hormone,thyroxine, insulin A-chain, insulin B-chain, proinsulin, relaxinA-chain, relaxin B-chain, prorelaxin, follicle stimulating hormone(FSH),thyroid stimulating hormone(TSH), leutinizing hormone(LH), glycoproteinhormone receptors, calcitonin, glucagon, factor VIII, an antibody, lungsurfactant, urokinase, streptokinase, human tissue-type plasminogenactivator (t-PA), bombesin, factor IX, thrombin, hemopoietic growthfactor, tumor necrosis factor-alpha and -beta, enkephalinase, humanserum albumin, mullerian-inhibiting substance, mousegonadotropin-associated peptide, β-lactamase, tissue factor protein,inhibin, activin, vascular endothelial growth factor, integrinreceptors, thrombopoietin, protein A or D, rheumatoid factors, NGF-β,platelet-growth factor, transforming growth factor; TGF-alpha andTGF-beta, insulin-like growth factor-I and -II, insulin-like growthfactor binding proteins, CD-4, DNase, latency associated peptide,erythropoietin, HER2 ligands, osteoinductive factors, interferon-alpha,-beta, and -gamma, colony stimulating factors (CSFs), M-CSF, GM-CSF, andG-CSF, interleukins (ILs), IL-1, IL-2, IL-3, IL-4, superoxide dismutase;decay accelerating factor, viral antigen, HIV envelope proteins GP120and GP140, atrial natriuretic peptides A, B, or C, or immuno globulins,and fragments of the above-listed proteins.
 8. The method of claim 7wherein the protein is a human protein.
 9. The method of claim 8 whereinthe protein comprises more than about 100 amino acid residues.
 10. Themethod of claim 1 wherein the protein comprises a plurality of rigidsecondary structures displaying amino acids capable of interacting withthe target, and the mutations are primarily produced at positionscorresponding to codons encoding the amino acids.
 11. The method ofclaim 10 wherein the rigid secondary structures comprise structuresselected from the group; α-(3.6₁₃)helix, 3₁₀ helix, π-(4.4₁₆)helix,parallel and anti-parallel β-pleated sheets, reverse turns, andnon-ordered structures.
 12. The method of claim 10 wherein the mutationsare produced at more than one codon.
 13. The method of claim 12 whereinthe mutations are produced on more than one rigid secondary structure.14. The method of claim 1 wherein the helper phage is selected from thegroup M13KO7, M13R408, M13-VCS, and Phi X
 174. 15. The method of claim14 wherein the helper phage is M13KO7 and the coat protein is the M13phage gene III coat protein.
 16. The method of claim 15 wherein the hostis E. coli.
 17. The method of claim 16 wherein the plasmid is undertight control of the transcription regulatory element.
 18. The method ofclaim 17 wherein the amount is less than about 1%.
 19. The method ofclaim 18 wherein the amount is less than 20% the amount of phagemidparticles displaying a single copy of the fusion protein.
 20. The methodof claim 19 wherein the amount is less than 10%.
 21. The method of claim1 further comprising in step (a), inserting a DNA triplet, encoding anmRNA suppressible terminator codon between said first gene encoding apolypeptide, and said second gene encoding at least a portion of a phagecoat protein.
 22. The method of claim 21 wherein said mRNA suppressibleterminator codon is selected from the following: UAG (amber), UAA(ocher) and UGA (opeI).
 23. The method of claim 22 wherein saidsuppressible mutation results in the detectable production of a fusionpolypeptide containing sadi polypeptide and said coat protein when saidexpression vector is grown in a suppressor host cell; and, when grown ina non-suppressor host cell said polypeptide is synthesized substantiallywithout fusion to said phage coat protein.
 24. A human growth hormonevariant wherein hGH amino acids 172, 174, 176 and 178 respectively areas a group sequentially selected from one of the following: (1)R,S,F,R;(2)R,A,Y,R; (3)K,T,Y,K; (4)R,S,Y,R; (5)K,A,Y,R; (6)R,F,F,R; (7)K,Q,Y,R;(8) R,T,Y,H; (9)Q,R,Y,R; (10)K,K,Y,K; (11)R,S,F,S; and (12)K,S,N,R. 25.A phagemid comprising a replicable expression vector comprising atranscription regulatory element operably linked to a gene fusionencoding a fusion protein wherein the gene fusion comprises a first geneencoding a polypeptide, and a second gene encoding at least a portion ofa phage coat protein, wherein a DNA triplet codon encoding an mRNAsuppressible terminator codon selected from UAG, UAA and UGA is insertedbetween the fused ends of the first and second genes, or is substitutedfor an amino acid encoding triplet codon adjacent to the gene fusionjunction.
 26. The phagemid of claim 25 wherein said first gene encodes amammalian protein.
 27. The phagemid of claim 26 wherein the protein isselected from the group: growth hormone, human growth hormone (hGH),des-N-methionyl human growth hormone, bovine growth hormone, parathyroidhormone, thyroxine, insulin A-chain, insulin B-chain, proinsulin,relaxin A-chain, relaxin B-chain, prorelaxin, follicle stimulatinghormone (FSH), thyroid stimulating hormone TSH), leutinizing hormone(LH), glycoprotein hormone receptors, calcitonin, glucagon, factor VIII,an antibody, lung surfactant, urokinase, streptokinase, humantissue-type plasminogen activator (t-PA), bombesin, factor IX, thrombin,hemopoietic growth factor, tumor necrosis factor-alpha and-beta,enkephalinase, human serum albumin, mullerian-inhibiting substance,mouse gonadotropin-associated peptide, β-lactamase, tissue factorprotein, inhibin, activin, vascular endothelial growth factor, integrinreceptors, thrombopoietin, protein A or D, rheumatoid factors, NGF-β,platelet-growth factor, transforming growth factor; TGF-alpha andTGF-beta, insulin-like growth-I and -II, insulin-like growth factorbinding proteins, CD-4, DNase, latency associated peptide,erythropoietin, osteoinductive factors, interferon-alpha, -beta, and-gamma, colony stimulating factors (CSFs), M-CSF, GM-CSF, and G-CSF,interleukins (ILs), IL-1, IL-2, IL-3, IL-4, superoxide dismutase; decayaccelerating factor, viral antigen, HIV envelope proteins GP120 andGP140, atrial natriuretic peptides A, B or C immuno globulins, andfragments of the above-listed proteins.
 28. The phagemid of claim 27wherein said protein is a human protein.
 29. The phagemid of claim 28wherein the protein comprises more than about 100 amino acid residues.30. The phagemid of claim 25 wherein said protein comprises a pluralityof rigid secondary structures displaying amino acids capable ofinteracting with the target.
 31. The phagemid of claim 30 wherein saidrigid secondary structures comprises structures selected from the group;α-(3.6₁₃)helix, 3₁₀ helix, π-(4.4₁₆)helix, parallel and anti-parallelβ-pleated sheets, reverse turns, and non-ordered structures.
 32. Thephagemid of claim 25 wherein the helper phage is selected from the groupM13KO7, M13R408, M13-VCS, and Phi X
 174. 33. The phagemid of claim 32wherein the helper phage is M13KO7 and the coat protein is the M13 phagegene III coat protein.
 34. The phagemid of claim 33 wherein the host isthe E. coli wild type or suppressor type.
 35. The phagemid of claim 34wherein the plasmid is under tight control of the transcriptionregulatory element.
 36. The phagemid of claim 35 wherein the number ofphagemid particles displaying more than one copy of the fusion proteinon the surface of the particles is less than 1%.
 37. The phagemid ofclaim 36 wherein said number of phagemid particles is less than about10%.
 38. The phagemid of claim 37 wherein the number of phagemidparticles is less than about 20%.
 39. A human growth variant wherein hGHamino acids 10, 14, 18, and 21 respectively are as a group sequentiallyselected from one of the following: (1)H,G,N,N; (2)A,W,D,N; (3)F,S,F,L;(4)Y,T,V,N and (5)I,N,I,N.
 40. A human growth variant wherein hGH aminoacids 174 is serine and 176 is tyrosine and hGH amino acids 167, 171,175 and 179 respectively are as a group sequentially selected from oneof the following: (1)N,S,T,T; (2)E,S,T,I; (3)K,S,T,L; (4)N,N,T,T; (5)R,D,I,I; and (6)N,S,T,Q.
 41. A method for selecting novel bindingpolypeptides comprising (a) constructing a replicable expression vectorcomprising a transcription regulatory element operably linked to DNAencoding a protein of interest containing one or more subunits, whereinthe DNA encoding at least one of the subunits is fused to the DNAencoding at least a portion of a phage coat protein; (b) mutating theDNA encoding the protein of interest at one or more selected positionsthereby forming a family of related vectors; (c) transforming suitablehost cells with the vectors; (d) infecting the transformed host cellswith a helper phage having a gene encoding the phage coat protein; (e)culturing the transformed infected host cells under conditions suitablefor forming recombinant phagemid particles containing at least a portionof the plasmid and capable of transforming the host, the conditionsadjusted so that no more than a minor amount of phagemid particlesdisplay more than one copy of the fusion protein on the surface of theparticle; (f) contacting the phagemid particles with a target moleculeso that at least a portion of the phagemid particles bind to the targetmolecule; and (g) separating the phagemid particles that bind from thosethat do not.
 42. The method of claim 41 wherein the expression vectorfurther comprises a secretory signal sequence operably linked to the DNAencoding each subunit of the protein of interest.
 43. The method ofclaim 42 wherein the protein of interest is a mammalian protein.
 44. Themethod of claim 43 wherein the protein of interest is selected from thegroup; insulin, relaxin, follicle stimulating hormone (FSH), thyroidstimulating hormone (TSH), leutinizing hormone (LH), glycoproteinhormone receptors, monoclonal and polyclonal antibodies, lungsurfactant, integrin receptors, insulin-like growth factor-I and -II,and. fragments of the above-listed proteins.
 45. The method of claim 44wherein the protein of interest is a humanized antibody.
 46. The methodof claim 45 wherein the protein of interest is a humanized Fab fragmentcapable of binding to the HER-2 receptor (human epidermal growth factorreceptor-2).
 47. A human growth hormone (hGH) variant wherein hGH aminoacid glutamate₁₇₄ is replaced by serine₁₇₄ and phenylalanine₁₇₆ isreplaced by tyrosine₁₇₆ and one or more of the eight naturally occurringhGH amino acids F10, M14, H18, H21, R167, D171, T175 and I179 arereplaced by another natural amino acid.
 48. The hGH variant of claim 47wherein the eight naturally occurring hGH amino acids F10, M14, H1 8,H21, R167, D171, T175 and I179 respectively are as a group replaced witha corresponding amino acid sequentially selected from one of thefollowing groups: (1) H, G, N, N, N, S, T, T; (2) H, G, N, N, E, S, T,I; (3) H, G, N, N, N, N, T, T; (4) A, W, D, N, N, S, T, T; (5) A, W, D,N, E, S, T, I; (6) A, W, D, N, N, N, T, T; (7) F, S, F, L, N, S, T, T;(8) F, S, F, L, E, S, T, I; (9) F, S, F, L, N, N, T, T. (10) H, G, N, N,N, S, T, N; (11) A, N, D, A, N, N, T, N; (12) F, S, F, G, H, S, T, T;(13) H, Q, T, S, A, D, N, S; (14) H, G, N, N, N, A, T, T; (15) F, S, F,L, S, D, T, T; (16) A, S, T, N, R, D, T, I; (17) Q, Y, N, N, H, S, T, T;(18) W, G, S, S, R, D, T, I; (19) F, L, S, S, K, N, T, V; (20) W, N, N,S, H, S, T, T; (21) A, N, A, S, N, S, T, T; (22) P, S, D, N, R, D, T, I;(23) H, G, N, N, N, N, T, S; (24) F, S, T, G, R, D, T, I; (25) M, T, S,N, Q, S, T, T; (26) F, S, F, L, T, S, T, S; (27) A, W, D, N, R, D, T, I;(28) A, W, D, N, H, S, T, N; (29) M, Q, M, N, N, S, T, T; (30) H, Y, D,H, R, D, T, T; (31) L, N, S, H, R, D, T, I; (32) L, N, S, H, T, S, T, T;(33) A, W, D, N, N, A, T, T; (34) F, S, T, G, R, D, T, I; (35) A, W, D,N, R, D, T, I; (36) I, Q, E, H, N, S, T, T; (37) F, S, L, A, N, S, T, V;(38) F, S, F, L, K, D, T, T; (39) M, A, D, N, N, S, T, T; (40) A, W, D,N, S, S, V, T; (41) H, Q, Y, S, R, D, T, I.


49. The method of claim 48 wherein said human growth hormone variant(11) further contains leucin₁₅ replaced by arginine₁₅ and lysine₁₆₈replaced by arginine₁₆₈.
 50. The method of claim 48 wherein said humangrowth hormone variant (40) further contains phenylalanine₁₇₆
 51. Amethod for selecting novel binding polypeptides comprising: (a)constructing a replicable expression vector comprising a transcriptionregulatory element operably linked to a gene fusion encoding a fusionprotein wherein the gene fusion comprises a first gene encoding apolypeptide operable connedted to a linking amino acid sequence, and asecond gene encoding at least a portion of a phage coat protein; (b)mutating the vector at one or more selected positions within the aminoacid linking sequence of the first gene thereby forming a family ofrelated plasmids; (c) transforming suitable host cells with theplasmids; (d) infecting the transformed host cells with a helper phagehaving a gene encoding the phage coat protein; (e) culturing thetransformed infected host cells under conditions suitable for formingrecombinant phagemid particles containing at least a portion of theplasmid and capable of transforming the host, the conditions adjusted sothat no more than a minor amount of phagemid particles display more thanone copy of the fusion protein on the surface of the particle; (f)contacting the phagemid particles with a target molecule so that atleast a portion of the phagemid particles bind to the target molecule;and (g) contacting the bound phagemid particles with a protease capableof hydrolysing the linking a aminio acid sequence of at least a portionof the bound phagmid particles, and (h) isolating the hydrolyzed phagmidparticles.
 52. The method of claim 51 further comprising infectingsuitable host cells with the hydrolyzed phagemid particles and repeatingsteps (d) through (h).